Query 028836
Match_columns 203
No_of_seqs 110 out of 143
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:18:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028836.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028836hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00633 HHH: Helix-hairpin-he 97.6 2.1E-05 4.6E-10 48.7 1.3 24 105-128 7-30 (30)
2 PRK01229 N-glycosylase/DNA lya 96.8 0.0086 1.9E-07 51.9 8.9 70 103-174 112-190 (208)
3 cd00056 ENDO3c endonuclease II 96.3 0.025 5.4E-07 45.1 7.9 38 105-144 79-117 (158)
4 COG0177 Nth Predicted EndoIII- 96.2 0.0056 1.2E-07 53.3 4.1 71 57-130 42-130 (211)
5 TIGR01084 mutY A/G-specific ad 95.7 0.047 1E-06 48.9 7.8 38 104-142 100-137 (275)
6 COG0122 AlkA 3-methyladenine D 95.6 0.042 9.1E-07 49.5 7.0 72 55-135 144-226 (285)
7 PRK10702 endonuclease III; Pro 95.2 0.031 6.7E-07 48.2 4.7 37 104-141 104-140 (211)
8 smart00478 ENDO3c endonuclease 95.1 0.043 9.4E-07 43.4 5.1 30 103-132 66-95 (149)
9 TIGR01083 nth endonuclease III 94.7 0.1 2.2E-06 43.8 6.4 39 104-143 101-139 (191)
10 PRK10880 adenine DNA glycosyla 94.6 0.049 1.1E-06 50.5 4.8 29 104-132 104-132 (350)
11 TIGR00588 ogg 8-oxoguanine DNA 94.5 0.033 7.1E-07 50.5 3.3 39 103-143 214-254 (310)
12 PRK13910 DNA glycosylase MutY; 94.3 0.064 1.4E-06 48.6 4.6 34 106-140 69-102 (289)
13 COG1194 MutY A/G-specific DNA 94.2 0.061 1.3E-06 50.0 4.4 36 108-143 112-147 (342)
14 PF02371 Transposase_20: Trans 94.1 0.042 9.1E-07 40.6 2.6 37 109-147 2-39 (87)
15 PRK13913 3-methyladenine DNA g 94.0 0.083 1.8E-06 46.1 4.6 40 106-146 118-157 (218)
16 TIGR03252 uncharacterized HhH- 94.0 0.044 9.4E-07 46.7 2.8 44 102-147 108-151 (177)
17 PRK10308 3-methyl-adenine DNA 94.0 0.059 1.3E-06 48.3 3.8 36 103-139 201-238 (283)
18 PRK02515 psbU photosystem II c 93.6 0.075 1.6E-06 43.5 3.3 38 105-147 57-94 (132)
19 smart00278 HhH1 Helix-hairpin- 92.0 0.12 2.6E-06 30.4 1.8 19 110-128 2-20 (26)
20 PF11731 Cdd1: Pathogenicity l 90.5 0.19 4.1E-06 38.8 2.1 26 104-129 7-32 (93)
21 PF10391 DNA_pol_lambd_f: Fing 88.6 0.29 6.3E-06 33.7 1.7 22 108-129 1-22 (52)
22 PF14716 HHH_8: Helix-hairpin- 86.9 0.92 2E-05 32.1 3.5 31 97-127 34-65 (68)
23 PRK14605 ruvA Holliday junctio 86.9 0.44 9.6E-06 40.6 2.2 30 103-132 67-96 (194)
24 TIGR01259 comE comEA protein. 86.0 0.9 2E-05 35.9 3.4 42 105-147 64-105 (120)
25 PF12826 HHH_2: Helix-hairpin- 84.3 2.4 5.1E-05 29.8 4.5 24 106-129 32-55 (64)
26 PRK00116 ruvA Holliday junctio 84.2 0.89 1.9E-05 38.4 2.8 27 105-131 69-95 (192)
27 KOG1921 Endonuclease III [Repl 83.9 1.7 3.6E-05 39.5 4.4 28 103-130 153-180 (286)
28 PRK14600 ruvA Holliday junctio 83.7 0.68 1.5E-05 39.4 1.8 30 103-132 67-96 (186)
29 TIGR00084 ruvA Holliday juncti 83.7 0.73 1.6E-05 39.2 2.0 29 103-131 66-94 (191)
30 PRK13901 ruvA Holliday junctio 83.5 0.71 1.5E-05 39.9 1.9 30 103-132 66-95 (196)
31 PF14520 HHH_5: Helix-hairpin- 82.8 1.2 2.7E-05 30.5 2.6 23 107-129 3-25 (60)
32 PRK00024 hypothetical protein; 82.1 7.1 0.00015 34.0 7.5 61 54-129 22-86 (224)
33 PRK14601 ruvA Holliday junctio 81.5 0.93 2E-05 38.6 1.9 30 103-132 67-96 (183)
34 TIGR00608 radc DNA repair prot 80.9 1.7 3.8E-05 37.8 3.4 62 54-129 12-80 (218)
35 COG2231 Uncharacterized protei 80.6 5.7 0.00012 35.0 6.4 67 107-174 113-197 (215)
36 COG2003 RadC DNA repair protei 80.0 3.5 7.6E-05 36.5 5.0 79 35-129 3-86 (224)
37 PF14520 HHH_5: Helix-hairpin- 78.4 1.2 2.7E-05 30.5 1.4 41 88-128 16-57 (60)
38 PRK14606 ruvA Holliday junctio 77.9 1.4 3.1E-05 37.5 1.8 29 104-132 68-96 (188)
39 KOG2875 8-oxoguanine DNA glyco 77.9 3.5 7.6E-05 38.1 4.5 32 104-135 213-246 (323)
40 PRK14602 ruvA Holliday junctio 77.4 1.6 3.5E-05 37.5 2.1 29 104-132 69-97 (203)
41 PF00416 Ribosomal_S13: Riboso 76.3 4 8.7E-05 31.5 3.8 40 106-145 12-54 (107)
42 TIGR00426 competence protein C 76.2 3.7 8E-05 28.7 3.3 39 108-147 15-54 (69)
43 COG1555 ComEA DNA uptake prote 75.8 2.6 5.5E-05 34.7 2.7 42 105-147 93-134 (149)
44 PRK14603 ruvA Holliday junctio 74.9 1.9 4.1E-05 36.9 1.8 29 104-132 67-95 (197)
45 COG0099 RpsM Ribosomal protein 72.4 3.4 7.4E-05 33.5 2.6 39 107-145 15-56 (121)
46 PRK14606 ruvA Holliday junctio 72.3 4.8 0.0001 34.3 3.7 99 54-164 62-167 (188)
47 COG1796 POL4 DNA polymerase IV 71.9 4.3 9.4E-05 37.8 3.5 71 103-174 45-131 (326)
48 PRK14601 ruvA Holliday junctio 71.8 5.1 0.00011 34.1 3.7 98 54-164 62-166 (183)
49 PRK14604 ruvA Holliday junctio 70.9 5.4 0.00012 34.2 3.7 99 54-164 62-173 (195)
50 PRK14604 ruvA Holliday junctio 70.6 2.7 5.9E-05 36.0 1.8 30 103-132 67-96 (195)
51 COG0353 RecR Recombinational D 70.6 3 6.5E-05 36.3 2.0 23 102-124 5-27 (198)
52 smart00279 HhH2 Helix-hairpin- 70.1 3.2 6.8E-05 26.5 1.6 15 113-127 20-34 (36)
53 PRK14603 ruvA Holliday junctio 70.0 6.2 0.00013 33.8 3.8 99 54-164 61-176 (197)
54 PRK13901 ruvA Holliday junctio 69.0 6.3 0.00014 34.1 3.7 64 54-127 61-125 (196)
55 PRK07945 hypothetical protein; 67.6 10 0.00022 34.7 5.0 19 110-128 50-68 (335)
56 COG0632 RuvA Holliday junction 67.3 3.5 7.6E-05 35.8 1.8 30 103-132 67-96 (201)
57 PF00356 LacI: Bacterial regul 65.6 15 0.00033 24.5 4.3 44 108-175 2-45 (46)
58 PF12836 HHH_3: Helix-hairpin- 65.5 2.9 6.2E-05 29.3 0.8 41 106-147 11-51 (65)
59 PRK14602 ruvA Holliday junctio 65.3 8.1 0.00018 33.2 3.7 99 54-164 63-179 (203)
60 PRK04053 rps13p 30S ribosomal 64.9 6.3 0.00014 32.7 2.8 57 102-158 18-80 (149)
61 CHL00137 rps13 ribosomal prote 62.7 8 0.00017 31.0 2.9 39 107-145 15-56 (122)
62 TIGR00084 ruvA Holliday juncti 62.1 8.7 0.00019 32.7 3.2 98 54-164 61-171 (191)
63 PRK00076 recR recombination pr 61.7 6.3 0.00014 34.1 2.3 22 104-125 6-27 (196)
64 PTZ00134 40S ribosomal protein 61.1 4.2 9.1E-05 34.0 1.1 54 101-154 22-81 (154)
65 cd00141 NT_POLXc Nucleotidyltr 60.7 6.9 0.00015 35.4 2.5 25 104-128 80-104 (307)
66 PF11798 IMS_HHH: IMS family H 60.5 5.4 0.00012 24.6 1.3 15 111-125 13-27 (32)
67 TIGR00615 recR recombination p 59.2 7.4 0.00016 33.7 2.3 22 104-125 6-27 (195)
68 TIGR03629 arch_S13P archaeal r 57.7 8.3 0.00018 31.8 2.3 36 108-143 20-58 (144)
69 TIGR03631 bact_S13 30S ribosom 57.5 10 0.00022 29.9 2.7 37 109-145 15-54 (113)
70 KOG2457 A/G-specific adenine D 57.2 5.2 0.00011 38.7 1.2 57 74-130 153-227 (555)
71 PRK13844 recombination protein 57.2 8.3 0.00018 33.6 2.3 22 104-125 10-31 (200)
72 PRK00116 ruvA Holliday junctio 56.7 75 0.0016 26.8 8.0 24 108-131 107-130 (192)
73 PRK05179 rpsM 30S ribosomal pr 56.6 11 0.00024 30.1 2.8 38 108-145 16-56 (122)
74 smart00483 POLXc DNA polymeras 55.4 11 0.00023 34.6 2.8 66 103-172 83-162 (334)
75 cd00080 HhH2_motif Helix-hairp 53.9 8.6 0.00019 27.8 1.6 19 111-129 24-42 (75)
76 cd00141 NT_POLXc Nucleotidyltr 53.5 10 0.00022 34.3 2.4 21 151-171 137-157 (307)
77 TIGR01339 phycocy_beta phycocy 52.8 17 0.00037 30.8 3.5 52 52-104 13-64 (170)
78 TIGR02417 fruct_sucro_rep D-fr 52.4 25 0.00054 30.3 4.5 48 108-176 2-49 (327)
79 smart00483 POLXc DNA polymeras 50.6 11 0.00024 34.5 2.1 36 98-133 37-72 (334)
80 COG3092 Uncharacterized protei 49.8 38 0.00082 28.1 4.9 51 80-131 28-81 (149)
81 TIGR00426 competence protein C 49.2 50 0.0011 22.9 4.9 22 107-128 45-66 (69)
82 PF00502 Phycobilisome: Phycob 46.6 14 0.00031 30.2 2.0 52 52-104 10-61 (157)
83 PRK14600 ruvA Holliday junctio 46.5 22 0.00048 30.3 3.2 98 54-164 62-169 (186)
84 PRK14605 ruvA Holliday junctio 45.9 16 0.00034 31.2 2.2 99 54-164 62-172 (194)
85 PRK14976 5'-3' exonuclease; Pr 45.4 12 0.00027 33.5 1.6 17 114-130 196-212 (281)
86 PRK10703 DNA-binding transcrip 44.5 42 0.00091 29.0 4.7 31 108-143 4-34 (341)
87 TIGR01259 comE comEA protein. 44.1 49 0.0011 26.0 4.6 21 107-127 96-116 (120)
88 PRK12766 50S ribosomal protein 41.8 19 0.00042 32.1 2.2 43 87-129 13-56 (232)
89 PRK09482 flap endonuclease-lik 41.5 16 0.00035 32.7 1.7 18 113-130 186-203 (256)
90 PRK11303 DNA-binding transcrip 40.6 50 0.0011 28.3 4.6 48 108-176 3-50 (328)
91 PRK08609 hypothetical protein; 40.3 30 0.00066 34.0 3.5 22 106-127 85-106 (570)
92 PF01367 5_3_exonuc: 5'-3' exo 38.1 5.9 0.00013 30.7 -1.4 16 114-129 23-38 (101)
93 cd00008 53EXOc 5'-3' exonuclea 37.4 21 0.00045 31.1 1.7 17 113-129 187-203 (240)
94 CHL00172 cpeB phycoerythrin be 37.3 38 0.00082 29.0 3.2 52 52-104 15-66 (177)
95 COG1059 Thermostable 8-oxoguan 36.9 1.5E+02 0.0032 26.2 6.7 69 107-175 118-193 (210)
96 CHL00090 apcD allophycocyanin 36.4 43 0.00094 28.0 3.4 50 53-103 15-64 (161)
97 smart00475 53EXOc 5'-3' exonuc 36.4 22 0.00047 31.6 1.7 18 113-130 190-207 (259)
98 PF14229 DUF4332: Domain of un 36.1 33 0.00072 27.0 2.5 26 106-131 50-75 (122)
99 CHL00170 cpcA phycocyanin alph 35.4 56 0.0012 27.5 3.9 52 52-104 15-66 (162)
100 CHL00086 apcA allophycocyanin 35.2 48 0.001 27.7 3.5 52 52-104 14-65 (161)
101 CHL00173 cpeA phycoerythrin al 35.0 44 0.00096 28.1 3.2 51 52-103 15-65 (164)
102 CHL00171 cpcB phycocyanin beta 33.9 44 0.00096 28.3 3.1 52 52-104 15-66 (172)
103 TIGR01338 phycocy_alpha phycoc 33.0 65 0.0014 27.1 3.9 52 52-104 14-65 (161)
104 PRK08609 hypothetical protein; 31.9 28 0.0006 34.3 1.8 32 98-129 110-143 (570)
105 PF04854 DUF624: Protein of un 31.7 22 0.00047 25.1 0.7 17 113-129 17-33 (77)
106 TIGR01954 nusA_Cterm_rpt trans 29.4 50 0.0011 21.0 2.2 42 87-128 3-45 (50)
107 PF14579 HHH_6: Helix-hairpin- 29.3 1.4E+02 0.003 21.9 4.8 32 111-144 29-60 (90)
108 PHA00439 exonuclease 29.0 75 0.0016 29.1 3.9 70 112-194 191-273 (286)
109 PRK12766 50S ribosomal protein 28.8 29 0.00062 31.0 1.2 20 109-128 3-22 (232)
110 COG3743 Uncharacterized conser 27.8 32 0.0007 28.3 1.2 20 109-128 67-86 (133)
111 TIGR01481 ccpA catabolite cont 26.9 1.2E+02 0.0026 26.0 4.7 45 108-176 4-48 (329)
112 PF05766 NinG: Bacteriophage L 26.8 1E+02 0.0023 26.6 4.2 38 137-174 148-187 (189)
113 PRK09672 phage exclusion prote 26.8 1.7E+02 0.0036 27.3 5.7 33 114-146 216-255 (305)
114 COG5578 Predicted integral mem 26.5 34 0.00073 30.0 1.2 12 114-125 37-48 (208)
115 PRK13482 DNA integrity scannin 25.9 55 0.0012 30.9 2.5 22 107-128 317-338 (352)
116 KOG1918 3-methyladenine DNA gl 25.8 52 0.0011 29.7 2.2 32 104-135 160-193 (254)
117 PHA01976 helix-turn-helix prot 25.2 51 0.0011 22.2 1.7 25 53-77 13-43 (67)
118 COG1980 Archaeal fructose 1,6- 25.2 22 0.00048 33.1 -0.2 73 83-162 62-148 (369)
119 COG0621 MiaB 2-methylthioadeni 25.2 63 0.0014 31.2 2.8 26 149-174 274-299 (437)
120 COG4989 Predicted oxidoreducta 25.0 43 0.00094 30.8 1.6 58 130-193 183-254 (298)
121 PRK03980 flap endonuclease-1; 23.7 45 0.00098 30.2 1.5 17 113-129 193-209 (292)
122 COG0632 RuvA Holliday junction 23.0 61 0.0013 28.2 2.1 20 108-127 107-126 (201)
123 PRK10423 transcriptional repre 22.8 1.3E+02 0.0028 25.7 4.1 30 109-143 2-31 (327)
124 TIGR03674 fen_arch flap struct 22.4 52 0.0011 30.2 1.7 17 113-129 240-256 (338)
125 PRK14350 ligA NAD-dependent DN 21.6 94 0.002 31.6 3.4 23 107-129 539-561 (669)
126 cd00128 XPG Xeroderma pigmento 21.5 57 0.0012 29.1 1.7 44 113-162 227-274 (316)
127 PRK00558 uvrC excinuclease ABC 21.5 93 0.002 31.0 3.3 22 108-129 542-563 (598)
128 PF14307 Glyco_tran_WbsX: Glyc 20.7 33 0.00071 31.3 -0.0 41 134-174 145-190 (345)
129 TIGR01448 recD_rel helicase, p 20.7 1.3E+02 0.0028 30.5 4.2 36 102-145 75-112 (720)
130 PRK14669 uvrC excinuclease ABC 20.6 1.4E+02 0.0031 30.1 4.3 21 109-129 552-572 (624)
131 PRK14671 uvrC excinuclease ABC 20.1 1.2E+02 0.0026 30.5 3.7 22 108-129 568-589 (621)
No 1
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=97.64 E-value=2.1e-05 Score=48.71 Aligned_cols=24 Identities=42% Similarity=0.700 Sum_probs=20.3
Q ss_pred HHHHHHhhcccCcChHHHHHHHhh
Q 028836 105 TKAVSELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 105 ~~Al~~Lt~LkGVGPATASaiLa~ 128 (203)
.+.++.|.+|+||||.||.+|++.
T Consensus 7 pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 7 PASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCHHHHHhCCCcCHHHHHHHHhC
Confidence 456889999999999999999974
No 2
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=96.80 E-value=0.0086 Score=51.93 Aligned_cols=70 Identities=27% Similarity=0.217 Sum_probs=52.1
Q ss_pred cHHHHHHHhh-cccCcChHHHHHHH-hhhCCCCCCcccHHHHHhhc---C----CCCCCCHHHHHHHHHHHHHHHHhcCc
Q 028836 103 DLTKAVSELT-VLKGVGPATASAVL-AAYAPGVAPFMSDEAMGAAL---G----HSKDYSLRQYLLFADKLQAKAKVSDI 173 (203)
Q Consensus 103 dv~~Al~~Lt-~LkGVGPATASaiL-a~~~P~~~pFfSDEa~~~~~---g----~~ikYt~keY~~~~~~l~~~a~el~~ 173 (203)
++..+.+.|. +||||||=|||.|| .+.. ..-|.-|--..-++ | .+..-|.+.|.+.-..+++.++.+|.
T Consensus 112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~--~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~ 189 (208)
T PRK01229 112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY--EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELGI 189 (208)
T ss_pred CchHHHHHHHHcCCCCcHHHHHHHHHHccC--CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcCC
Confidence 5678899999 99999999999999 4544 21344665443332 4 12245679999999999999999988
Q ss_pred c
Q 028836 174 F 174 (203)
Q Consensus 174 ~ 174 (203)
.
T Consensus 190 ~ 190 (208)
T PRK01229 190 S 190 (208)
T ss_pred C
Confidence 7
No 3
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=96.28 E-value=0.025 Score=45.12 Aligned_cols=38 Identities=37% Similarity=0.437 Sum_probs=29.3
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhC-CCCCCcccHHHHHh
Q 028836 105 TKAVSELTVLKGVGPATASAVLAAYA-PGVAPFMSDEAMGA 144 (203)
Q Consensus 105 ~~Al~~Lt~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~ 144 (203)
..+.+.|++||||||-||+.+|.... ++.+|. |-...-
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~r 117 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVRR 117 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHHH
Confidence 67899999999999999999998743 445453 665543
No 4
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=96.21 E-value=0.0056 Score=53.31 Aligned_cols=71 Identities=24% Similarity=0.280 Sum_probs=46.4
Q ss_pred CHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHH-HH------------hhC-----ccHHHHHHHhhcccCcC
Q 028836 57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEK-AF------------KSL-----PDLTKAVSELTVLKGVG 118 (203)
Q Consensus 57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~-Af------------~~l-----~dv~~Al~~Lt~LkGVG 118 (203)
|.|+.++-+-=+|- +..|+...+...+.++ +++.++. +| +++ .++..+++.|.+|+|||
T Consensus 42 ttD~~vn~at~~Lf--~~~~t~e~l~~a~~~~-l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVG 118 (211)
T COG0177 42 TTDEVVNKATPALF--KRYPTPEDLLNADEEE-LEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG 118 (211)
T ss_pred CchHHHHHHHHHHH--HHcCCHHHHHcCCHHH-HHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence 46777766665554 2345666666655444 4444332 22 011 15677899999999999
Q ss_pred hHHHHHHHhhhC
Q 028836 119 PATASAVLAAYA 130 (203)
Q Consensus 119 PATASaiLa~~~ 130 (203)
+-||..+|+...
T Consensus 119 rKTAnvVL~~a~ 130 (211)
T COG0177 119 RKTANVVLSFAF 130 (211)
T ss_pred hHHHHHHHHhhc
Confidence 999999999854
No 5
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=95.69 E-value=0.047 Score=48.92 Aligned_cols=38 Identities=29% Similarity=0.385 Sum_probs=28.7
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM 142 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~ 142 (203)
+...++.|++|+||||-||++||+...-...|+ -|--.
T Consensus 100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~~v 137 (275)
T TIGR01084 100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDGNV 137 (275)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chHhH
Confidence 345789999999999999999999865433344 55544
No 6
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.56 E-value=0.042 Score=49.48 Aligned_cols=72 Identities=28% Similarity=0.256 Sum_probs=53.1
Q ss_pred CCCHHHHHHHHHHHhh-CCCCCcchhhhhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhcccCcChHHHHHH
Q 028836 55 HINTTELSKLVRWKLT-RGKWRPRLLDFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV 125 (203)
Q Consensus 55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~--------dv~~Al~~Lt~LkGVGPATASai 125 (203)
+.|-++|..+=++-|+ -|..+.+ .+.+.++++...+-.+ +...+++.|++||||||=||-.+
T Consensus 144 fptpe~l~~~~~~~l~~~g~s~~K---------a~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~ 214 (285)
T COG0122 144 FPTPEQLAAADEEALRRCGLSGRK---------AEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMF 214 (285)
T ss_pred CCCHHHHHhcCHHHHHHhCCcHHH---------HHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHH
Confidence 6888998888888886 5665553 3455556655554322 46779999999999999999999
Q ss_pred Hhh--hCCCCCC
Q 028836 126 LAA--YAPGVAP 135 (203)
Q Consensus 126 La~--~~P~~~p 135 (203)
|-. ..|+.+|
T Consensus 215 llf~lgr~dvfP 226 (285)
T COG0122 215 LLFGLGRPDVFP 226 (285)
T ss_pred HHHcCCCCCCCC
Confidence 876 4676655
No 7
>PRK10702 endonuclease III; Provisional
Probab=95.18 E-value=0.031 Score=48.17 Aligned_cols=37 Identities=27% Similarity=0.286 Sum_probs=27.9
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHH
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEA 141 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa 141 (203)
+..+.+.|.+|+||||-||.+||....-. ..|.-|--
T Consensus 104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~ 140 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTH 140 (211)
T ss_pred CCchHHHHhcCCcccHHHHHHHHHHHcCC-Ccccccch
Confidence 45688999999999999999999986532 23444443
No 8
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.14 E-value=0.043 Score=43.40 Aligned_cols=30 Identities=37% Similarity=0.386 Sum_probs=25.0
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
++....+.|++|+||||-||+++|...--.
T Consensus 66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~ 95 (149)
T smart00478 66 EVPDDREELLKLPGVGRKTANAVLSFALGK 95 (149)
T ss_pred CccHHHHHHHcCCCCcHHHHHHHHHHHCCC
Confidence 344678899999999999999999986544
No 9
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=94.70 E-value=0.1 Score=43.76 Aligned_cols=39 Identities=28% Similarity=0.225 Sum_probs=28.4
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (203)
+..+.+.|++||||||-||.+||....-.. -|.-|--..
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~ 139 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVF 139 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHH
Confidence 445788999999999999999998864321 245555443
No 10
>PRK10880 adenine DNA glycosylase; Provisional
Probab=94.64 E-value=0.049 Score=50.54 Aligned_cols=29 Identities=31% Similarity=0.454 Sum_probs=25.1
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
+....+.|.+|+||||-||++||+...-.
T Consensus 104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~ 132 (350)
T PRK10880 104 FPETFEEVAALPGVGRSTAGAILSLSLGK 132 (350)
T ss_pred chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence 45678999999999999999999986643
No 11
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=94.54 E-value=0.033 Score=50.48 Aligned_cols=39 Identities=28% Similarity=0.370 Sum_probs=31.0
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHH
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSDEAMG 143 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~ 143 (203)
+...+.+.|++||||||-||.+||.. ..|+.+| .|-...
T Consensus 214 ~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~P--vD~~v~ 254 (310)
T TIGR00588 214 SYEDAREALCELPGVGPKVADCICLMGLDKPQAVP--VDVHVW 254 (310)
T ss_pred ChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCcee--ecHHHH
Confidence 35678999999999999999999977 4566666 375553
No 12
>PRK13910 DNA glycosylase MutY; Provisional
Probab=94.29 E-value=0.064 Score=48.58 Aligned_cols=34 Identities=26% Similarity=0.262 Sum_probs=26.2
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHH
Q 028836 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDE 140 (203)
Q Consensus 106 ~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDE 140 (203)
...+.|.+|+||||-||.+||+...-..++ .-|-
T Consensus 69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~-~VD~ 102 (289)
T PRK13910 69 NDYQSLLKLPGIGAYTANAILCFGFREKSA-CVDA 102 (289)
T ss_pred hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC-cccH
Confidence 468999999999999999999986543323 3444
No 13
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.21 E-value=0.061 Score=50.04 Aligned_cols=36 Identities=33% Similarity=0.437 Sum_probs=28.3
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 028836 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (203)
.+.|.+|+||||-||+||||...-...|+..--+..
T Consensus 112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~R 147 (342)
T COG1194 112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKR 147 (342)
T ss_pred HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchhe
Confidence 456777999999999999999876667766655554
No 14
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.12 E-value=0.042 Score=40.61 Aligned_cols=37 Identities=32% Similarity=0.496 Sum_probs=29.7
Q ss_pred HHhhcccCcChHHHHHHHhhh-CCCCCCcccHHHHHhhcC
Q 028836 109 SELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMGAALG 147 (203)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~-~P~~~pFfSDEa~~~~~g 147 (203)
+.|+.++||||-||..||+.. +|+ -|=+...+...+|
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~--rF~~~~~l~~~~G 39 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDIS--RFKSAKQLASYAG 39 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCch--hcccchhhhhccc
Confidence 468899999999999999986 443 4667788877666
No 15
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=94.04 E-value=0.083 Score=46.09 Aligned_cols=40 Identities=23% Similarity=0.163 Sum_probs=28.9
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhc
Q 028836 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL 146 (203)
Q Consensus 106 ~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~ 146 (203)
...+.|.+||||||=||.+||....- ..-|..|.-..-++
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv~ 157 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLFL 157 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHHH
Confidence 45688999999999999999987542 32456666554443
No 16
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=94.01 E-value=0.044 Score=46.70 Aligned_cols=44 Identities=27% Similarity=0.342 Sum_probs=32.3
Q ss_pred ccHHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcC
Q 028836 102 PDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (203)
Q Consensus 102 ~dv~~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (203)
|+-....+.|.+|+||||-||..+|+...-+- -.-||-|....|
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~--~~~~~~~~~~~~ 151 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQL--GVTPEGWREAAG 151 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh--CCCCcchHHhcc
Confidence 44556688999999999999999999765431 145677765554
No 17
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=94.01 E-value=0.059 Score=48.34 Aligned_cols=36 Identities=28% Similarity=0.294 Sum_probs=29.3
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccH
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSD 139 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfSD 139 (203)
+...+++.|++||||||-||..||-. ..|+.+| -.|
T Consensus 201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp-~~D 238 (283)
T PRK10308 201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDD 238 (283)
T ss_pred CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC-ccc
Confidence 56778999999999999999999865 5787655 444
No 18
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=93.57 E-value=0.075 Score=43.47 Aligned_cols=38 Identities=24% Similarity=0.327 Sum_probs=32.4
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcC
Q 028836 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (203)
Q Consensus 105 ~~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (203)
.+..+.|..|+||||++|..|.. +.||-|=|-...+.|
T Consensus 57 ~A~~~el~~lpGigP~~A~~IV~-----nGpf~sveDL~~V~G 94 (132)
T PRK02515 57 NSSVRAFRQFPGMYPTLAGKIVK-----NAPYDSVEDVLNLPG 94 (132)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHH-----CCCCCCHHHHHcCCC
Confidence 34567889999999999999993 669999998888887
No 19
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=92.02 E-value=0.12 Score=30.40 Aligned_cols=19 Identities=47% Similarity=0.763 Sum_probs=16.9
Q ss_pred HhhcccCcChHHHHHHHhh
Q 028836 110 ELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 110 ~Lt~LkGVGPATASaiLa~ 128 (203)
.|.+++|||+.+|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 4789999999999999974
No 20
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=90.46 E-value=0.19 Score=38.79 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=22.2
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhh
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~ 129 (203)
..+.+..|+.|+|||||||-=+..++
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LG 32 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLG 32 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence 34578899999999999999888774
No 21
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=88.56 E-value=0.29 Score=33.71 Aligned_cols=22 Identities=36% Similarity=0.351 Sum_probs=17.3
Q ss_pred HHHhhcccCcChHHHHHHHhhh
Q 028836 108 VSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~ 129 (203)
|+.++++-||||+||.-..+.+
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G 22 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKG 22 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT
T ss_pred CcchhhcccccHHHHHHHHHhC
Confidence 5789999999999999888764
No 22
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=86.91 E-value=0.92 Score=32.07 Aligned_cols=31 Identities=32% Similarity=0.415 Sum_probs=22.6
Q ss_pred HHhhCccHHHHHHH-hhcccCcChHHHHHHHh
Q 028836 97 AFKSLPDLTKAVSE-LTVLKGVGPATASAVLA 127 (203)
Q Consensus 97 Af~~l~dv~~Al~~-Lt~LkGVGPATASaiLa 127 (203)
+.+.+|..-..++. +.+|+|||+.+|.-|--
T Consensus 34 ~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 34 AIKALPYPITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred HHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 34556755555575 99999999999988743
No 23
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.85 E-value=0.44 Score=40.62 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=26.1
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
+-+.-+..|.+..||||-||-+||+.+.|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence 456678899999999999999999998775
No 24
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=85.95 E-value=0.9 Score=35.85 Aligned_cols=42 Identities=29% Similarity=0.468 Sum_probs=33.8
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcC
Q 028836 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (203)
Q Consensus 105 ~~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (203)
.+..+.|..|+||||.+|..|+.-..- ..||-|-|-+..+.|
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~-~g~f~s~eeL~~V~G 105 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYREE-NGAFKSVDDLTKVSG 105 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHcCCC
Confidence 345778999999999999999998653 558888777776765
No 25
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=84.29 E-value=2.4 Score=29.78 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.8
Q ss_pred HHHHHhhcccCcChHHHHHHHhhh
Q 028836 106 KAVSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 106 ~Al~~Lt~LkGVGPATASaiLa~~ 129 (203)
+..+.|++++||||.+|..|....
T Consensus 32 a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 32 ASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp --HHHHCTSTT--HHHHHHHHHHH
T ss_pred cCHHHHhccCCcCHHHHHHHHHHH
Confidence 467889999999999999998764
No 26
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=84.23 E-value=0.89 Score=38.44 Aligned_cols=27 Identities=33% Similarity=0.541 Sum_probs=22.4
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhCC
Q 028836 105 TKAVSELTVLKGVGPATASAVLAAYAP 131 (203)
Q Consensus 105 ~~Al~~Lt~LkGVGPATASaiLa~~~P 131 (203)
+.....|..++||||.||-.||+.+.+
T Consensus 69 k~~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 69 RELFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 345778899999999999999988655
No 27
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=83.92 E-value=1.7 Score=39.53 Aligned_cols=28 Identities=32% Similarity=0.491 Sum_probs=26.0
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYA 130 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~ 130 (203)
|+...++.|..|+||||-+|=+.|++.-
T Consensus 153 DIP~~v~dLlsLPGVGPKMa~L~m~~AW 180 (286)
T KOG1921|consen 153 DIPDTVEDLLSLPGVGPKMAHLTMQVAW 180 (286)
T ss_pred CCchhHHHHhcCCCCchHHHHHHHHHHh
Confidence 7889999999999999999999999853
No 28
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.70 E-value=0.68 Score=39.43 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=25.2
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
+-+.-+..|.+..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 456677888999999999999999987775
No 29
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=83.68 E-value=0.73 Score=39.20 Aligned_cols=29 Identities=34% Similarity=0.568 Sum_probs=23.8
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAP 131 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P 131 (203)
+-+.-+..|...+||||-||-+||+...|
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL~~~~~ 94 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAILSNMSP 94 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence 34667788889999999999999988766
No 30
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.50 E-value=0.71 Score=39.85 Aligned_cols=30 Identities=27% Similarity=0.378 Sum_probs=25.8
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
+-+.-+..|.+..||||-||-+|||...|+
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs~~~~~ 95 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLSGIKYN 95 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 456678889999999999999999998875
No 31
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=82.80 E-value=1.2 Score=30.46 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=20.3
Q ss_pred HHHHhhcccCcChHHHHHHHhhh
Q 028836 107 AVSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa~~ 129 (203)
....|..++||||.+|..+....
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G 25 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAG 25 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTT
T ss_pred HHHhhccCCCCCHHHHHHHHhcC
Confidence 45778899999999999999984
No 32
>PRK00024 hypothetical protein; Reviewed
Probab=82.06 E-value=7.1 Score=33.98 Aligned_cols=61 Identities=28% Similarity=0.442 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH----HHHHHHhhcccCcChHHHHHHHhhh
Q 028836 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL----TKAVSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv----~~Al~~Lt~LkGVGPATASaiLa~~ 129 (203)
..|+-.||..++ |..|..|. .|....++-++...++ .+..+.|++++|||||.|..|+++.
T Consensus 22 ~~Lsd~ELLa~l---L~~g~~~~------------~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~ 86 (224)
T PRK00024 22 AALSDAELLAIL---LRTGTKGK------------SVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAAL 86 (224)
T ss_pred ccCCHHHHHHHH---HcCCCCCC------------CHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHH
Confidence 588888865543 56665443 4555555544433332 3346789999999999999998883
No 33
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.54 E-value=0.93 Score=38.59 Aligned_cols=30 Identities=30% Similarity=0.345 Sum_probs=23.9
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
+-+.-+..|.+..||||-||-+|||...|+
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs~~~~~ 96 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCSSLDVN 96 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 345677888888888888888888887775
No 34
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.91 E-value=1.7 Score=37.79 Aligned_cols=62 Identities=27% Similarity=0.340 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhcccCcChHHHHHHH
Q 028836 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL 126 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~------l~dv-~~Al~~Lt~LkGVGPATASaiL 126 (203)
..|+-.||..++ |.-|.-|.. .|.+.+++-++. +.++ .+..+.|++.+|||||.|..|+
T Consensus 12 ~~Lsd~ELLail---L~~g~~~~~-----------~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 12 EALSDYELLAII---LRTGTPKGL-----------DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred ccCCHHHHHHHH---HhCCCCCCC-----------CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence 578888966554 555653320 344444433332 2232 3457889999999999999999
Q ss_pred hhh
Q 028836 127 AAY 129 (203)
Q Consensus 127 a~~ 129 (203)
++.
T Consensus 78 a~~ 80 (218)
T TIGR00608 78 AAV 80 (218)
T ss_pred HHH
Confidence 983
No 35
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=80.64 E-value=5.7 Score=35.05 Aligned_cols=67 Identities=27% Similarity=0.305 Sum_probs=40.7
Q ss_pred HHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhc---C-CCC-CCC-H------------HHHHHHHHHHHHHH
Q 028836 107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL---G-HSK-DYS-L------------RQYLLFADKLQAKA 168 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~---g-~~i-kYt-~------------keY~~~~~~l~~~a 168 (203)
.-+.|-++||||+-||=+||--.. ++.-|.-|..-.-+. | ... +|+ + ..|.+|..-++..+
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~-~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~~l~~~~~lyqe~HAlIv~~~ 191 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYAL-DRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFEENLPENLRLYQEFHALIVEHA 191 (215)
T ss_pred HHHHHHccCCcchhhHHHHHHHHh-cCcccchhHHHHHHHHHhcccccccHHHHHHHHHhcchhHHHHHHHHHHHHHHHH
Confidence 456788999999999999987643 343566666544332 3 222 454 2 23555555555666
Q ss_pred HhcCcc
Q 028836 169 KVSDIF 174 (203)
Q Consensus 169 ~el~~~ 174 (203)
++....
T Consensus 192 K~f~~k 197 (215)
T COG2231 192 KHFCKK 197 (215)
T ss_pred HHHccC
Confidence 554444
No 36
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=80.01 E-value=3.5 Score=36.51 Aligned_cols=79 Identities=25% Similarity=0.348 Sum_probs=52.3
Q ss_pred hhhhHhhhhchh-hhcCCCCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhC---ccHH-HHHH
Q 028836 35 LDDYYRKELPSL-IHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSL---PDLT-KAVS 109 (203)
Q Consensus 35 LD~w~~~elp~~-~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l---~dv~-~Al~ 109 (203)
+.+|...+.|.- +.. .....|+-.||.-++ |+.|..+- .|...++.-++.+ ..+. +.++
T Consensus 3 i~~~~~~~rPRErll~-~G~~~Lsd~ELLail---LrtG~~~~------------~~~~la~~lL~~fg~L~~l~~a~~~ 66 (224)
T COG2003 3 IKDNPENERPRERLLK-LGAEALSDAELLAIL---LRTGTKGE------------SVLDLAKELLQEFGSLAELLKASVE 66 (224)
T ss_pred ccccccccchHHHHHH-hChhhcchHHHHHHH---HhcCCCCC------------CHHHHHHHHHHHcccHHHHHhCCHH
Confidence 345665555532 111 123589999976665 67776433 5666666665544 3444 4599
Q ss_pred HhhcccCcChHHHHHHHhhh
Q 028836 110 ELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 110 ~Lt~LkGVGPATASaiLa~~ 129 (203)
.||.++|||+|-|.=+.++.
T Consensus 67 el~~v~GiG~aka~~l~a~~ 86 (224)
T COG2003 67 ELSSVKGIGLAKAIQIKAAI 86 (224)
T ss_pred HHhhCCCccHHHHHHHHHHH
Confidence 99999999999999988873
No 37
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=78.44 E-value=1.2 Score=30.46 Aligned_cols=41 Identities=29% Similarity=0.458 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhh
Q 028836 88 SSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 88 ~~V~~~t~~Af~~l~dv~~-Al~~Lt~LkGVGPATASaiLa~ 128 (203)
..++.....+|..+.|+.. ..+.|.+++||||.+|.-|...
T Consensus 16 ~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 16 KRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHH
T ss_pred HHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHH
Confidence 3344444444443333322 4677999999999999988764
No 38
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.94 E-value=1.4 Score=37.51 Aligned_cols=29 Identities=21% Similarity=0.267 Sum_probs=21.6
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
-+.-+..|++..||||-||-+||+...|+
T Consensus 68 Er~lF~~Li~V~GIGpK~AL~iLs~~~~~ 96 (188)
T PRK14606 68 KKELFLSLTKVSRLGPKTALKIISNEDAE 96 (188)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 45567777788888888888888876664
No 39
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=77.93 E-value=3.5 Score=38.08 Aligned_cols=32 Identities=28% Similarity=0.389 Sum_probs=25.5
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhh--hCCCCCC
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAA--YAPGVAP 135 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~--~~P~~~p 135 (203)
.+.|-++||.|+||||-.|-+|+-. .-++.+|
T Consensus 213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP 246 (323)
T KOG2875|consen 213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVP 246 (323)
T ss_pred HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc
Confidence 4669999999999999999987644 4555666
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.40 E-value=1.6 Score=37.47 Aligned_cols=29 Identities=28% Similarity=0.403 Sum_probs=23.0
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
-+.-+..|.+..||||-||-+||+...|+
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 45567788888888888888888887764
No 41
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=76.33 E-value=4 Score=31.49 Aligned_cols=40 Identities=23% Similarity=0.279 Sum_probs=29.9
Q ss_pred HHHHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHhh
Q 028836 106 KAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (203)
Q Consensus 106 ~Al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~ 145 (203)
.-.-+|++++|||+.+|..|+... +|. .+-.++|+-+..+
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l 54 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKL 54 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHH
Confidence 345578999999999999999984 564 5566788766543
No 42
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=76.15 E-value=3.7 Score=28.73 Aligned_cols=39 Identities=28% Similarity=0.432 Sum_probs=28.9
Q ss_pred HHHhhc-ccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcC
Q 028836 108 VSELTV-LKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (203)
Q Consensus 108 l~~Lt~-LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (203)
.+.|.. ++|||+.+|.+|+.-... ..+|-+-+.+..++|
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~-~g~~~s~~dL~~v~g 54 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREE-YGPFKTVEDLKQVPG 54 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHH-cCCcCCHHHHHcCCC
Confidence 346777 999999999999998643 336667666666655
No 43
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=75.79 E-value=2.6 Score=34.68 Aligned_cols=42 Identities=31% Similarity=0.517 Sum_probs=32.2
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcC
Q 028836 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (203)
Q Consensus 105 ~~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (203)
.+..+.|..|+||||+.|-+|.+--.- ..||=|=|=..-+.|
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~-~G~f~sv~dL~~v~G 134 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREE-NGPFKSVDDLAKVKG 134 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHH-cCCCCcHHHHHhccC
Confidence 445777899999999999999998543 448877776665655
No 44
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.87 E-value=1.9 Score=36.94 Aligned_cols=29 Identities=34% Similarity=0.441 Sum_probs=23.6
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
-+.-+..|.+..||||-||-+||+...|+
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~ 95 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSALPPA 95 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 45567788889999999999999987774
No 45
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=72.42 E-value=3.4 Score=33.46 Aligned_cols=39 Identities=21% Similarity=0.292 Sum_probs=30.8
Q ss_pred HHHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHhh
Q 028836 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~ 145 (203)
-.=+||.++|||+++|-+|+... +|+ .+-..+||-...+
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred EeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 34468999999999999999984 565 6677888877644
No 46
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.33 E-value=4.8 Score=34.27 Aligned_cols=99 Identities=16% Similarity=0.164 Sum_probs=59.7
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
.+.|++|..-.-.-.--.| -=| +-+.+++..+++.+.++... .=.+.||+++|||+-||.-|.-=.-..
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~AL~iLs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 62 GFSNERKKELFLSLTKVSR-LGPKTALKIISNEDAETLVTMIAS---------QDVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 4788888655444433333 223 34566666677766655543 135689999999999999876421110
Q ss_pred ----CC--CcccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 133 ----VA--PFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 133 ----~~--pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
.. .-..+|+..++. ...|+.++=..-+..+
T Consensus 132 ~~~~~~~~~~~~~e~~~AL~--~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 132 FESAGIKDMRIYHESLEALV--SLGYPEKQAREAVKHV 167 (188)
T ss_pred hccccCCCcccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 00 012367777776 3678877766655554
No 47
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=71.86 E-value=4.3 Score=37.79 Aligned_cols=71 Identities=20% Similarity=0.192 Sum_probs=44.7
Q ss_pred cHHHHHHH--hhcccCcChHHHHHHHhhhCCCCCCcccHHHH----------HhhcCCCCCCCHHHHHHH----HHHHHH
Q 028836 103 DLTKAVSE--LTVLKGVGPATASAVLAAYAPGVAPFMSDEAM----------GAALGHSKDYSLRQYLLF----ADKLQA 166 (203)
Q Consensus 103 dv~~Al~~--Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~----------~~~~g~~ikYt~keY~~~----~~~l~~ 166 (203)
|+....+. +|+|+|||++||+.|--..+-..++ +-++.- .-++|-+-+=-.+-|..+ .+.+++
T Consensus 45 ~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~-~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~ 123 (326)
T COG1796 45 DLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVK-KLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGIKDLEELQE 123 (326)
T ss_pred chHHHHhhcccCCCCCccHHHHHHHHHHHHcCccH-HHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHCcccHHHHHH
Confidence 67777777 9999999999999998775544444 222211 123342233345566666 466777
Q ss_pred HHHhcCcc
Q 028836 167 KAKVSDIF 174 (203)
Q Consensus 167 ~a~el~~~ 174 (203)
-++.+.++
T Consensus 124 a~~~~~~~ 131 (326)
T COG1796 124 ALENGKIR 131 (326)
T ss_pred HHHhCCcc
Confidence 77766666
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.77 E-value=5.1 Score=34.12 Aligned_cols=98 Identities=20% Similarity=0.229 Sum_probs=59.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCC-
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~~P- 131 (203)
.+.|++|..-...-.--.| -=| +-+..++..+++.+.++.... =.+.|++++||||-||.=|+-=.-.
T Consensus 62 GF~~~~Er~lF~~Li~VsG-IGpK~Al~ILs~~~~~el~~aI~~~---------D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 62 GFLDKDEQKMFEMLLKVNG-IGANTAMAVCSSLDVNSFYKALSLG---------DESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 4788888665444433333 233 235566666777666555431 2568999999999999987632111
Q ss_pred -----CCCCcccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 132 -----GVAPFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 132 -----~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
...+ -.+|+..++.+ ..|+.++=...+..+
T Consensus 132 ~~~~~~~~~-~~~ea~~AL~~--LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 132 KTKLENVSD-DKSEALAALLT--LGFKQEKIIKVLASC 166 (183)
T ss_pred hhccCCCCc-cHHHHHHHHHH--cCCCHHHHHHHHHhc
Confidence 1111 13677777763 678877776666554
No 49
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.94 E-value=5.4 Score=34.17 Aligned_cols=99 Identities=18% Similarity=0.151 Sum_probs=57.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
.+.|++|..-...-.--.| -=| +-+.+++..+++.+.++... .=.+.|++++||||-||--|..=....
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~Al~iLs~~~~~el~~aI~~---------~D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 62 GFSTPAQRQLFELLIGVSG-VGPKAALNLLSSGTPDELQLAIAG---------GDVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 5789998665554433333 223 23555566666666555443 124679999999999999876532111
Q ss_pred C-----------CC-cccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 133 V-----------AP-FMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 133 ~-----------~p-FfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
. .+ --.+|+..++. ...|+.++=..-+..+
T Consensus 132 ~~~~~~~~~~~~~~~~~~~e~~~aL~--~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 132 IDVRQLSGSTSPAVSALDRELSEILI--SLGYSAAEAAAAIAAL 173 (195)
T ss_pred hccccccccccccccccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 0 00 01156666655 3667777666655544
No 50
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.63 E-value=2.7 Score=35.97 Aligned_cols=30 Identities=27% Similarity=0.383 Sum_probs=26.2
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
+-+.-+..|.+..||||=||-+||+...|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 96 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLSSGTPD 96 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 346678899999999999999999998775
No 51
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=70.60 E-value=3 Score=36.34 Aligned_cols=23 Identities=39% Similarity=0.700 Sum_probs=19.5
Q ss_pred ccHHHHHHHhhcccCcChHHHHH
Q 028836 102 PDLTKAVSELTVLKGVGPATASA 124 (203)
Q Consensus 102 ~dv~~Al~~Lt~LkGVGPATASa 124 (203)
|.+..-|+.|.+|+||||-||.=
T Consensus 5 ~~i~~LI~~l~kLPGvG~KsA~R 27 (198)
T COG0353 5 PPIEKLIDALKKLPGVGPKSAQR 27 (198)
T ss_pred HHHHHHHHHHhhCCCCChhHHHH
Confidence 35677899999999999999974
No 52
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=70.12 E-value=3.2 Score=26.48 Aligned_cols=15 Identities=47% Similarity=0.729 Sum_probs=13.2
Q ss_pred cccCcChHHHHHHHh
Q 028836 113 VLKGVGPATASAVLA 127 (203)
Q Consensus 113 ~LkGVGPATASaiLa 127 (203)
-++||||.||--+|.
T Consensus 20 Gv~giG~ktA~~ll~ 34 (36)
T smart00279 20 GVKGIGPKTALKLLR 34 (36)
T ss_pred CCCcccHHHHHHHHH
Confidence 589999999998875
No 53
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.00 E-value=6.2 Score=33.83 Aligned_cols=99 Identities=18% Similarity=0.126 Sum_probs=56.4
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
.+.|++|..-.-.-.--.| -=| +-+..++..+++.+.+++... =.+.|++++||||-||.-|..=.-..
T Consensus 61 GF~~~~Er~lF~~L~~V~G-IGpK~AL~iLs~~~~~~l~~aI~~~---------D~~~L~kvpGIGkKtAerIilELkdK 130 (197)
T PRK14603 61 GFPDEDSLELFELLLGVSG-VGPKLALALLSALPPALLARALLEG---------DARLLTSASGVGKKLAERIALELKGK 130 (197)
T ss_pred CcCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 4788888654444332233 233 345666666777666555442 24679999999999999876321100
Q ss_pred ---------------C-CCcccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 133 ---------------V-APFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 133 ---------------~-~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
. ..--.+|+..++. ...|+-++=...+..+
T Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~ea~~AL~--~LGy~~~ea~~al~~i 176 (197)
T PRK14603 131 VPEHLLAGPAGGGGTKVSSTAAEDAVLALL--ALGFREAQVRSVVAEL 176 (197)
T ss_pred hhhhcccccccccccccCCccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 0 0001256666554 3567776666555544
No 54
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.96 E-value=6.3 Score=34.05 Aligned_cols=64 Identities=17% Similarity=0.310 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHh
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLA 127 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa 127 (203)
.+.|++|..-.-.-.--.| -=| +-+..++..+++.+.++... .=.+.||+++|||+-||.=|.-
T Consensus 61 GF~t~~Er~lF~~LisVsG-IGPK~ALaILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 61 GFLNSSEREVFEELIGVDG-IGPRAALRVLSGIKYNEFRDAIDR---------EDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHH
Confidence 4788888665544433333 223 34566666677766655543 1356899999999999997764
No 55
>PRK07945 hypothetical protein; Provisional
Probab=67.65 E-value=10 Score=34.70 Aligned_cols=19 Identities=47% Similarity=0.733 Sum_probs=14.9
Q ss_pred HhhcccCcChHHHHHHHhh
Q 028836 110 ELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 110 ~Lt~LkGVGPATASaiLa~ 128 (203)
.|++|+|||..||..|--.
T Consensus 50 ~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred CcccCCCcCHHHHHHHHHH
Confidence 5778888888888877654
No 56
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=67.26 E-value=3.5 Score=35.75 Aligned_cols=30 Identities=27% Similarity=0.458 Sum_probs=26.3
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
+-+.-+..|.+.-||||-||=+|||..+|+
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~ 96 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPE 96 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHH
Confidence 456678899999999999999999998875
No 57
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=65.59 E-value=15 Score=24.47 Aligned_cols=44 Identities=23% Similarity=0.269 Sum_probs=30.1
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHhcCccc
Q 028836 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKVSDIFF 175 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l~~~a~el~~~~ 175 (203)
|+.+.++-||.++|.|-+|.=. +-+|+|.- +++.+.++++|+.+
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~-----~~vs~~tr-------------------~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP-----PRVSEETR-------------------ERILEAAEELGYRP 45 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC-----SSSTHHHH-------------------HHHHHHHHHHTB-S
T ss_pred HHHHHHHHCcCHHHHHHHHhCC-----CCCCHHHH-------------------HHHHHHHHHHCCCC
Confidence 5567778899999999998742 44565543 45666667777664
No 58
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=65.50 E-value=2.9 Score=29.28 Aligned_cols=41 Identities=32% Similarity=0.488 Sum_probs=27.4
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcC
Q 028836 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (203)
Q Consensus 106 ~Al~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (203)
+..+.|..|+||||.+|-.|+..-.- .-||-|=|=+..+.|
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R~~-~G~f~s~~dL~~v~g 51 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYREK-NGPFKSLEDLKEVPG 51 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHHHH-H-S-SSGGGGGGSTT
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHh-CcCCCCHHHHhhCCC
Confidence 45788999999999999999998532 347777666665555
No 59
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.33 E-value=8.1 Score=33.19 Aligned_cols=99 Identities=13% Similarity=0.152 Sum_probs=57.1
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
.+.|.+|..-...-.--.|- =| +-+.+++..+++.+.++.... =.+.|++++|||+-||.-|..=.-..
T Consensus 63 GF~~~~Er~lF~~Li~V~GI-GpK~Al~iLs~~~~~~l~~aI~~~---------D~~~L~~ipGIGkKtAerIilELkdK 132 (203)
T PRK14602 63 GFATWDERQTFIVLISISKV-GAKTALAILSQFRPDDLRRLVAEE---------DVAALTRVSGIGKKTAQHIFLELKYK 132 (203)
T ss_pred CCCCHHHHHHHHHHhCCCCc-CHHHHHHHHhhCCHHHHHHHHHhC---------CHHHHhcCCCcCHHHHHHHHHHHHHh
Confidence 47888886655544333331 23 345666666666665554431 25689999999999999876321100
Q ss_pred ----------------CCC-cccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 133 ----------------VAP-FMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 133 ----------------~~p-FfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
..+ -..+|+..++. ...|+.++=..-+.++
T Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~ea~~AL~--~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 133 LKVEGLPAAAVLAGTGAVPGSVFRDALAGLA--NLGYGEEEARPVLKEV 179 (203)
T ss_pred hccccccccccccccccCCCchHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 000 11256666654 3667777766555544
No 60
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=64.87 E-value=6.3 Score=32.71 Aligned_cols=57 Identities=23% Similarity=0.358 Sum_probs=37.4
Q ss_pred ccHHHHHHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHhh---cCCCCCCCHHHHH
Q 028836 102 PDLTKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSLRQYL 158 (203)
Q Consensus 102 ~dv~~Al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~---~g~~ikYt~keY~ 158 (203)
|+-+.-.-+|+.+.|||+.+|-.|+.-. +|. .+--.+++-...+ ...+-+|..++|.
T Consensus 18 ~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~ 80 (149)
T PRK04053 18 DGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWM 80 (149)
T ss_pred CCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhh
Confidence 3334444568999999999999999884 555 4556777765433 2344555555554
No 61
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=62.73 E-value=8 Score=30.98 Aligned_cols=39 Identities=26% Similarity=0.360 Sum_probs=29.1
Q ss_pred HHHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHhh
Q 028836 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~ 145 (203)
..-+|+.+.|||+.||-.|+... +|. .+--.+|+-+..+
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l 56 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISAL 56 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHH
Confidence 34468999999999999999984 565 4556777766543
No 62
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=62.06 E-value=8.7 Score=32.66 Aligned_cols=98 Identities=21% Similarity=0.205 Sum_probs=53.4
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~~P~ 132 (203)
.+.|++|..-...-.--.|- =| +-+.+++.-+++.+.++..+. =.+.|+++||||+-||.-|+--....
T Consensus 61 GF~~~~Er~lF~~L~~V~GI-GpK~Al~iL~~~~~~el~~aI~~~---------d~~~L~~ipGiGkKtAerIileLk~k 130 (191)
T TIGR00084 61 GFNTLEERELFKELIKVNGV-GPKLALAILSNMSPEEFVYAIETE---------EVKALVKIPGVGKKTAERLLLELKGK 130 (191)
T ss_pred CCCCHHHHHHHHHHhCCCCC-CHHHHHHHHhcCCHHHHHHHHHhC---------CHHHHHhCCCCCHHHHHHHHHHHHhh
Confidence 47899997665554433331 12 223334443444433333221 12468999999999999987321100
Q ss_pred ------------CCCcccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 133 ------------VAPFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 133 ------------~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
..+ ..+|+..++. ...|+.++=..-+.++
T Consensus 131 ~~~~~~~~~~~~~~~-~~~e~~~aL~--~LGy~~~e~~~ai~~~ 171 (191)
T TIGR00084 131 LKGNKNLEMFTPTEA-ARDELFEALV--SLGYKPQEIQQALKKI 171 (191)
T ss_pred hcccccccccccccc-hHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 112 2356666555 3667777766655554
No 63
>PRK00076 recR recombination protein RecR; Reviewed
Probab=61.70 E-value=6.3 Score=34.14 Aligned_cols=22 Identities=32% Similarity=0.641 Sum_probs=18.8
Q ss_pred HHHHHHHhhcccCcChHHHHHH
Q 028836 104 LTKAVSELTVLKGVGPATASAV 125 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASai 125 (203)
+..-++.|.+|+||||-||.=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRL 27 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5677889999999999999754
No 64
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=61.06 E-value=4.2 Score=33.98 Aligned_cols=54 Identities=19% Similarity=0.208 Sum_probs=35.5
Q ss_pred CccHHHHHHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHh---hcCCCCCCCH
Q 028836 101 LPDLTKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGA---ALGHSKDYSL 154 (203)
Q Consensus 101 l~dv~~Al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~---~~g~~ikYt~ 154 (203)
+|+-+...-+|+.++|||+.+|-.|++.. +|. .+--.+|+=... +...+.+|.+
T Consensus 22 l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~i 81 (154)
T PTZ00134 22 VDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKI 81 (154)
T ss_pred CCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCC
Confidence 44445556678999999999999999984 554 444566665543 2334445543
No 65
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=60.67 E-value=6.9 Score=35.37 Aligned_cols=25 Identities=28% Similarity=0.392 Sum_probs=20.3
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhh
Q 028836 104 LTKAVSELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASaiLa~ 128 (203)
...+|..|++++||||.||-.+...
T Consensus 80 ~~~~l~~l~~i~GiGpk~a~~l~~l 104 (307)
T cd00141 80 VPPGLLLLLRVPGVGPKTARKLYEL 104 (307)
T ss_pred chHHHHHHHcCCCCCHHHHHHHHHc
Confidence 4567888889999999999888843
No 66
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=60.54 E-value=5.4 Score=24.61 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=11.4
Q ss_pred hhcccCcChHHHHHH
Q 028836 111 LTVLKGVGPATASAV 125 (203)
Q Consensus 111 Lt~LkGVGPATASai 125 (203)
+.++.|||+.|+--+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 568999999998654
No 67
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.25 E-value=7.4 Score=33.73 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=18.8
Q ss_pred HHHHHHHhhcccCcChHHHHHH
Q 028836 104 LTKAVSELTVLKGVGPATASAV 125 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASai 125 (203)
+..-++.|.+|+||||-||.=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5667889999999999999754
No 68
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=57.74 E-value=8.3 Score=31.76 Aligned_cols=36 Identities=28% Similarity=0.419 Sum_probs=27.2
Q ss_pred HHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHH
Q 028836 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMG 143 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~ 143 (203)
.-+|+.++|||+.+|-.|+... +|. .+--.+|+-..
T Consensus 20 ~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~ 58 (144)
T TIGR03629 20 EYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIE 58 (144)
T ss_pred EEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHH
Confidence 3468999999999999999884 554 45557777554
No 69
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=57.50 E-value=10 Score=29.94 Aligned_cols=37 Identities=24% Similarity=0.381 Sum_probs=28.7
Q ss_pred HHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHhh
Q 028836 109 SELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (203)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~ 145 (203)
-.|+.+.|||+.+|-.|+... +|. .+-..+|+-+..+
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 54 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAI 54 (113)
T ss_pred eeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 457999999999999999884 565 5567777766543
No 70
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=57.25 E-value=5.2 Score=38.70 Aligned_cols=57 Identities=21% Similarity=0.256 Sum_probs=33.7
Q ss_pred CCcchhhhhhhCCHHHHHHHHH-HHH---------------hhCcc-HHHHHHHhhc-ccCcChHHHHHHHhhhC
Q 028836 74 WRPRLLDFVSSLDDSSVKSASE-KAF---------------KSLPD-LTKAVSELTV-LKGVGPATASAVLAAYA 130 (203)
Q Consensus 74 fRP~L~~lV~sN~~~~V~~~t~-~Af---------------~~l~d-v~~Al~~Lt~-LkGVGPATASaiLa~~~ 130 (203)
.=|+|..+....=+..|.+.-. -+| ..++. +...-+.|.+ ++||||-||-||+|...
T Consensus 153 kwPTl~dla~Asl~~eVn~lWaGlGyY~R~rrL~ega~~vv~~~~ge~Prta~~l~kgvpGVG~YTAGAiaSIAf 227 (555)
T KOG2457|consen 153 KWPTLYDLAQASLEKEVNELWAGLGYYRRARRLLEGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIAF 227 (555)
T ss_pred hCchHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHhhCCCCCccchhhhhhhhh
Confidence 3588888876555555554321 111 11111 2223344555 99999999999999853
No 71
>PRK13844 recombination protein RecR; Provisional
Probab=57.16 E-value=8.3 Score=33.56 Aligned_cols=22 Identities=14% Similarity=0.374 Sum_probs=18.6
Q ss_pred HHHHHHHhhcccCcChHHHHHH
Q 028836 104 LTKAVSELTVLKGVGPATASAV 125 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASai 125 (203)
+..-++.|.+|+||||-||.=+
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rl 31 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRL 31 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5667889999999999999754
No 72
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=56.74 E-value=75 Score=26.78 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=20.4
Q ss_pred HHHhhcccCcChHHHHHHHhhhCC
Q 028836 108 VSELTVLKGVGPATASAVLAAYAP 131 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P 131 (203)
.+.|++++|||+.||-.|+.-+..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHH
Confidence 557899999999999999977543
No 73
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=56.65 E-value=11 Score=30.15 Aligned_cols=38 Identities=32% Similarity=0.443 Sum_probs=28.6
Q ss_pred HHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHhh
Q 028836 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~ 145 (203)
.-+|+.+.|||+.+|-.|+.-. +|. .+--.+|+-+..+
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 56 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKI 56 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 3467999999999999999984 565 4566777766543
No 74
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=55.36 E-value=11 Score=34.63 Aligned_cols=66 Identities=17% Similarity=0.118 Sum_probs=41.8
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCCC------CC--cccHHHHHhhcC------CCCCCCHHHHHHHHHHHHHHH
Q 028836 103 DLTKAVSELTVLKGVGPATASAVLAAYAPGV------AP--FMSDEAMGAALG------HSKDYSLRQYLLFADKLQAKA 168 (203)
Q Consensus 103 dv~~Al~~Lt~LkGVGPATASaiLa~~~P~~------~p--FfSDEa~~~~~g------~~ikYt~keY~~~~~~l~~~a 168 (203)
.+..+|..|.+++||||.||-.+-..+ -.+ .+ .++.+- ..| -..+....|-..+.+.+.+..
T Consensus 83 ~~p~~l~~l~~i~GiGpk~a~~l~~lG-i~tl~eL~~a~~~~l~~~q---~~gl~~~~~~~~ri~r~e~~~i~~~i~~~l 158 (334)
T smart00483 83 EVYKSLKLFTNVFGVGPKTAAKWYRKG-IRTLEELKKNKELKLTKQQ---KAGLKYYEDILKKVSRAEAFAVEYIVKRAV 158 (334)
T ss_pred cHHHHHHHHHccCCcCHHHHHHHHHhC-CCCHHHHHhcccccCCHHH---HHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence 467799999999999999998887742 111 00 233322 112 234566677777777777777
Q ss_pred HhcC
Q 028836 169 KVSD 172 (203)
Q Consensus 169 ~el~ 172 (203)
+.+.
T Consensus 159 ~~~~ 162 (334)
T smart00483 159 RKIL 162 (334)
T ss_pred HhhC
Confidence 6654
No 75
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=53.88 E-value=8.6 Score=27.80 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=16.1
Q ss_pred hhcccCcChHHHHHHHhhh
Q 028836 111 LTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 111 Lt~LkGVGPATASaiLa~~ 129 (203)
+..++||||-||.-+|.-+
T Consensus 24 i~gv~giG~k~A~~ll~~~ 42 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEY 42 (75)
T ss_pred CCCCCcccHHHHHHHHHHh
Confidence 3458999999999999874
No 76
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=53.54 E-value=10 Score=34.28 Aligned_cols=21 Identities=10% Similarity=0.104 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHHHHHHHHHhc
Q 028836 151 DYSLRQYLLFADKLQAKAKVS 171 (203)
Q Consensus 151 kYt~keY~~~~~~l~~~a~el 171 (203)
+....|...+.+.+.+..+.+
T Consensus 137 ri~r~ea~~~a~~i~~~l~~~ 157 (307)
T cd00141 137 RIPREEALAIAEIIKEALREV 157 (307)
T ss_pred CeEHHHHHHHHHHHHHHHHhC
Confidence 344455555555565555554
No 77
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=52.79 E-value=17 Score=30.82 Aligned_cols=52 Identities=17% Similarity=0.337 Sum_probs=46.2
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (203)
..+|++..||.+|-.. +..|..|...-+.+.+|.+..|.++.++-|...|++
T Consensus 13 ~gRyl~~~eL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~l 64 (170)
T TIGR01339 13 RGEFISSSQIDALSKL-VADGNKRSDAVSRITNNASTIVTNAARSLFAEQPQL 64 (170)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCCC
Confidence 3579999999998776 578999999999999999999999999999988853
No 78
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=52.40 E-value=25 Score=30.25 Aligned_cols=48 Identities=21% Similarity=0.161 Sum_probs=31.2
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHhcCcccc
Q 028836 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKVSDIFFF 176 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l~~~a~el~~~~~ 176 (203)
|+-+.++-||.++|.|-+|.= .|.. .-.|+ +-.+++.+.++|||+.+|
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~-~~~~-~~vs~-------------------~tr~rV~~~a~~lgY~pn 49 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING-KAKE-YRISQ-------------------ETVERVMAVVREQGYQPN 49 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC-CCCC-CccCH-------------------HHHHHHHHHHHHhCCCCC
Confidence 455677889999999999962 1110 01333 344677777788887754
No 79
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=50.65 E-value=11 Score=34.54 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=25.7
Q ss_pred HhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 028836 98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGV 133 (203)
Q Consensus 98 f~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~~P~~ 133 (203)
++.+|..-..+..+++|+|||+++|+-|--...-..
T Consensus 37 i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~ 72 (334)
T smart00483 37 LKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGK 72 (334)
T ss_pred HHhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCc
Confidence 345553333456789999999999999987765443
No 80
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.79 E-value=38 Score=28.14 Aligned_cols=51 Identities=22% Similarity=0.288 Sum_probs=35.7
Q ss_pred hhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhc---ccCcChHHHHHHHhhhCC
Q 028836 80 DFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTV---LKGVGPATASAVLAAYAP 131 (203)
Q Consensus 80 ~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~---LkGVGPATASaiLa~~~P 131 (203)
+|---=++..|.++|+-|.+.+|-+. .+..+.. =+.+|||.|+|+.++.-|
T Consensus 28 rL~pvFpEnRVikaTrfairfMP~vA-vftl~wQ~~~~~ql~pAv~tAlfal~lp 81 (149)
T COG3092 28 RLAPVFPENRVIKATRFAIRFMPPVA-VFTLCWQIALGGQLGPAVATALFALSLP 81 (149)
T ss_pred hhcccCchhHHHHHHHHHHHhccHHH-HHHHHHHHHHhcccchHHHHHHHHHhcc
Confidence 33334468899999999999888542 2332222 237999999999998554
No 81
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=49.17 E-value=50 Score=22.89 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=17.2
Q ss_pred HHHHhhcccCcChHHHHHHHhh
Q 028836 107 AVSELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa~ 128 (203)
.++.|.+++|||+.||--|+..
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhh
Confidence 4566777889999999887754
No 82
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=46.58 E-value=14 Score=30.23 Aligned_cols=52 Identities=21% Similarity=0.257 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (203)
..+|++..||..|-.+- ..|.-|....+.+++|.+.-|.++.++-|...|++
T Consensus 10 egRyls~~EL~~l~~~~-~~~~~Rl~aa~~L~~~a~~IV~~A~~~l~~~~P~l 61 (157)
T PF00502_consen 10 EGRYLSDGELQALKGYF-QSANARLEAAEKLRDNASEIVDQAAQKLFEKYPDL 61 (157)
T ss_dssp TTSECEHHHHHHHHHHH-HTHHHHHHHHHHHHHTHHHHHHHHHHHHHHHSGGG
T ss_pred cCCCCCHHHHHHHHHHH-HhHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcccc
Confidence 35799999999998875 45777999999999999999999999999888853
No 83
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.47 E-value=22 Score=30.25 Aligned_cols=98 Identities=17% Similarity=0.208 Sum_probs=57.8
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhh---
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY--- 129 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiLa~~--- 129 (203)
.+.|++|..-.-.-.--.| -=| +-+.+++..+++.+.++..+. | .+.| +++|||+-||.-|+.=.
T Consensus 62 GF~~~~Er~lF~~LisV~G-IGpK~Al~iLs~~~~~~l~~aI~~~-----D----~~~L-~vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 62 GFLNREEQDCLRMLVKVSG-VNYKTAMSILSKLTPEQLFSAIVNE-----D----KAAL-KVNGIGEKLINRIITELQYK 130 (186)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHccCCHHHHHHHHHcC-----C----Hhhe-ECCCCcHHHHHHHHHHHHHH
Confidence 4788888665544433333 223 345566666666666555441 2 3567 89999999999887321
Q ss_pred ----CCCC-CC-cccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 130 ----APGV-AP-FMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 130 ----~P~~-~p-FfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
.+.. .+ --.+|+..++.+ ..|+.++=..-+.++
T Consensus 131 ~~~~~~~~~~~~~~~~e~~~aL~~--LGy~~~ea~~al~~v 169 (186)
T PRK14600 131 VSKLEINETNFIIINDDALAALIS--LGYEKTKAFNAIQKI 169 (186)
T ss_pred hhccccccccccccHHHHHHHHHH--cCCCHHHHHHHHHHh
Confidence 1111 00 013677776663 678888866666555
No 84
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.91 E-value=16 Score=31.15 Aligned_cols=99 Identities=20% Similarity=0.227 Sum_probs=53.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhhhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHH------
Q 028836 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL------ 126 (203)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~Al~~Lt~LkGVGPATASaiL------ 126 (203)
.+.|++|-.-.-.-.--.|- =| +-+..++.-+++.+.++... .=.+.|++++|||+-||--|.
T Consensus 62 GF~~~~Er~lF~~Li~V~GI-GpK~Al~ILs~~~~~~l~~aI~~---------~D~~~L~~vpGIGkKtAerIilELk~K 131 (194)
T PRK14605 62 GFATTEELSLFETLIDVSGI-GPKLGLAMLSAMNAEALASAIIS---------GNAELLSTIPGIGKKTASRIVLELKDK 131 (194)
T ss_pred CCCCHHHHHHHHHHhCCCCC-CHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 47888886554444333332 22 33455555555554433322 124579999999999999843
Q ss_pred --hhhCCC---CCCcccHHHHHhhcCCCCCCCHHHHHHHHHHH
Q 028836 127 --AAYAPG---VAPFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (203)
Q Consensus 127 --a~~~P~---~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (203)
....+. ..+-..+|++.++.+ ..|+.++=...+..+
T Consensus 132 i~~~~~~~~~~~~~~~~~e~~~aL~~--LGy~~~~a~~ai~~~ 172 (194)
T PRK14605 132 IAKNWEAGVLSQVTEANSDILATLTA--LGYSSSEAAKAISSL 172 (194)
T ss_pred HHhhhhccccccccchHHHHHHHHHH--cCCCHHHHHHHHHHh
Confidence 211110 011123677766653 567666655554444
No 85
>PRK14976 5'-3' exonuclease; Provisional
Probab=45.43 E-value=12 Score=33.49 Aligned_cols=17 Identities=47% Similarity=0.874 Sum_probs=14.9
Q ss_pred ccCcChHHHHHHHhhhC
Q 028836 114 LKGVGPATASAVLAAYA 130 (203)
Q Consensus 114 LkGVGPATASaiLa~~~ 130 (203)
++||||-||..+|.-+.
T Consensus 196 VpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 196 VKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCcccHHHHHHHHHHcC
Confidence 79999999999998753
No 86
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=44.47 E-value=42 Score=29.05 Aligned_cols=31 Identities=23% Similarity=0.427 Sum_probs=23.4
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 028836 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (203)
|+-+.++-||..+|.|-+|.= -|..|+|.-.
T Consensus 4 i~dIA~~agVS~~TVSrvLn~-----~~~vs~~tr~ 34 (341)
T PRK10703 4 IKDVAKRAGVSTTTVSHVINK-----TRFVAEETRN 34 (341)
T ss_pred HHHHHHHhCCCHHHHHHHHcC-----CCCCCHHHHH
Confidence 556677779999999999952 2568888743
No 87
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=44.09 E-value=49 Score=25.97 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=16.8
Q ss_pred HHHHhhcccCcChHHHHHHHh
Q 028836 107 AVSELTVLKGVGPATASAVLA 127 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa 127 (203)
.++.|.+++||||.|+--|.-
T Consensus 96 s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 96 SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHHcCCCCCHHHHHHHHh
Confidence 467778899999999877653
No 88
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=41.78 E-value=19 Score=32.08 Aligned_cols=43 Identities=33% Similarity=0.443 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhhCccHHHH-HHHhhcccCcChHHHHHHHhhh
Q 028836 87 DSSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 87 ~~~V~~~t~~Af~~l~dv~~A-l~~Lt~LkGVGPATASaiLa~~ 129 (203)
+...+..-..+|..+.++..| .+.|.+++|||+++|--|....
T Consensus 13 ~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 13 PSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred HHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 344555555557666676655 8999999999999999999874
No 89
>PRK09482 flap endonuclease-like protein; Provisional
Probab=41.52 E-value=16 Score=32.66 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=15.8
Q ss_pred cccCcChHHHHHHHhhhC
Q 028836 113 VLKGVGPATASAVLAAYA 130 (203)
Q Consensus 113 ~LkGVGPATASaiLa~~~ 130 (203)
-.+||||.||.-+|.-+.
T Consensus 186 GVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCcChHHHHHHHHHhC
Confidence 389999999999999854
No 90
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=40.64 E-value=50 Score=28.32 Aligned_cols=48 Identities=25% Similarity=0.234 Sum_probs=31.6
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHhcCcccc
Q 028836 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKVSDIFFF 176 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l~~~a~el~~~~~ 176 (203)
|+-+.++-||.++|.|-+|.= .|.. +-.|+| -.+++.+.++|||+.+|
T Consensus 3 i~dIA~~aGVS~~TVSrvLn~-~~~~-~~Vs~~-------------------tr~rV~~~a~elgY~pn 50 (328)
T PRK11303 3 LDEIARLAGVSRTTASYVING-KAKQ-YRVSDK-------------------TVEKVMAVVREHNYHPN 50 (328)
T ss_pred HHHHHHHhCCCHHHHHHHHcC-CCCC-CCcCHH-------------------HHHHHHHHHHHhCCCCC
Confidence 556777889999999999963 2210 123433 44667777777777754
No 91
>PRK08609 hypothetical protein; Provisional
Probab=40.29 E-value=30 Score=34.02 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=15.8
Q ss_pred HHHHHhhcccCcChHHHHHHHh
Q 028836 106 KAVSELTVLKGVGPATASAVLA 127 (203)
Q Consensus 106 ~Al~~Lt~LkGVGPATASaiLa 127 (203)
.++..|++++||||.||-.+-.
T Consensus 85 ~~~~~l~~i~GiGpk~a~~l~~ 106 (570)
T PRK08609 85 EGLLPLLKLPGLGGKKIAKLYK 106 (570)
T ss_pred HHHHHHhcCCCCCHHHHHHHHH
Confidence 3566777788888888877663
No 92
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=38.05 E-value=5.9 Score=30.70 Aligned_cols=16 Identities=44% Similarity=0.910 Sum_probs=13.9
Q ss_pred ccCcChHHHHHHHhhh
Q 028836 114 LKGVGPATASAVLAAY 129 (203)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (203)
.+||||-||+-+|.-+
T Consensus 23 V~GIG~KtA~~LL~~y 38 (101)
T PF01367_consen 23 VPGIGPKTAAKLLQEY 38 (101)
T ss_dssp -TTSTCHCCCCCHHHH
T ss_pred CCCCCHHHHHHHHHHc
Confidence 7899999999999975
No 93
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=37.40 E-value=21 Score=31.08 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=14.9
Q ss_pred cccCcChHHHHHHHhhh
Q 028836 113 VLKGVGPATASAVLAAY 129 (203)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (203)
-++||||-||.-+|.-+
T Consensus 187 Gv~GiG~ktA~~Ll~~~ 203 (240)
T cd00008 187 GVPGIGEKTAAKLLKEY 203 (240)
T ss_pred CCCccCHHHHHHHHHHh
Confidence 38999999999999875
No 94
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=37.33 E-value=38 Score=29.05 Aligned_cols=52 Identities=17% Similarity=0.193 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (203)
..+||+.+||.+|-. -+..|..|-..-+.+.+|...-|.++.++-|...|++
T Consensus 15 qgRYLs~~eL~~L~~-~~~~g~~RL~aa~~L~~NA~~IV~~A~~~l~~~~P~l 66 (177)
T CHL00172 15 KAAYVGGSDLQALKK-FISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPGL 66 (177)
T ss_pred ccCCCCHHHHHHHHH-HHHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCCC
Confidence 357999999999855 4688999999999999999999999999999988853
No 95
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=36.89 E-value=1.5e+02 Score=26.23 Aligned_cols=69 Identities=22% Similarity=0.241 Sum_probs=48.9
Q ss_pred HHHHhh-cccCcChHHHHHHHhhhCCCCCCcccHHHHHhhc--C----CCCCCCHHHHHHHHHHHHHHHHhcCccc
Q 028836 107 AVSELT-VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL--G----HSKDYSLRQYLLFADKLQAKAKVSDIFF 175 (203)
Q Consensus 107 Al~~Lt-~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~--g----~~ikYt~keY~~~~~~l~~~a~el~~~~ 175 (203)
|=+.|. ++||+|=--||=.|-=.-=+.+....--...|+. | .|...|.|-|+..-+.+++.|+++|+++
T Consensus 118 aRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~g~s~ 193 (210)
T COG1059 118 ARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEVGISL 193 (210)
T ss_pred HHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHhCCCc
Confidence 555666 8999999999998863221222222222334554 3 3458899999999999999999999984
No 96
>CHL00090 apcD allophycocyanin gamma subunit
Probab=36.44 E-value=43 Score=27.96 Aligned_cols=50 Identities=20% Similarity=0.317 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCcc
Q 028836 53 NPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (203)
Q Consensus 53 ~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (203)
.+|+|..||..|-.+ +..|.-|-..-+.+++|.+.-|.++.++-|...|+
T Consensus 15 gRyls~~EL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~ 64 (161)
T CHL00090 15 LRYPTIGELESIQDY-LKTGEKRIRIATILRDNEKEIIQKASKQLFQIHPE 64 (161)
T ss_pred cCCCCHHHHHHHHHH-HHhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHCcC
Confidence 479999999999776 57788899999999999999999999999988874
No 97
>smart00475 53EXOc 5'-3' exonuclease.
Probab=36.36 E-value=22 Score=31.55 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=15.3
Q ss_pred cccCcChHHHHHHHhhhC
Q 028836 113 VLKGVGPATASAVLAAYA 130 (203)
Q Consensus 113 ~LkGVGPATASaiLa~~~ 130 (203)
-++||||-||.-+|.=+.
T Consensus 190 GV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 190 GVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCHHHHHHHHHHhC
Confidence 379999999999998753
No 98
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=36.05 E-value=33 Score=26.98 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=22.2
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCC
Q 028836 106 KAVSELTVLKGVGPATASAVLAAYAP 131 (203)
Q Consensus 106 ~Al~~Lt~LkGVGPATASaiLa~~~P 131 (203)
.++.-|+.++||||..|-++..++-.
T Consensus 50 ~~~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 50 VNQADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HhHHHhhhcCCCCHHHHHHHHHhCcC
Confidence 36777889999999999999999753
No 99
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=35.43 E-value=56 Score=27.55 Aligned_cols=52 Identities=12% Similarity=0.155 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (203)
..+|++..||..|.. -+.+|..|-..-+.+.+|...-|.++.++-|+..|++
T Consensus 15 qgRyls~~eL~~l~~-~~~~g~~RL~aa~~Lt~nA~~IV~~Aa~~lf~~~P~l 66 (162)
T CHL00170 15 QGRFLSNGELQACNG-RFQRAAASLEAARSLTSNAQRLIDGAAQAVYTKFPYT 66 (162)
T ss_pred ccCCCCHHHHHHHHH-HHhccHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcCc
Confidence 357999999999866 4678999999999999999999999999999988853
No 100
>CHL00086 apcA allophycocyanin alpha subunit
Probab=35.24 E-value=48 Score=27.71 Aligned_cols=52 Identities=19% Similarity=0.411 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (203)
..+|++..||..|-.. +..|..|-..-+.+.+|.+.-|.++.++-|...|++
T Consensus 14 ~gRyls~~eL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~l 65 (161)
T CHL00086 14 EARYLSPGELDRIKSF-VLSGQRRLRIAQILTDNRERIVKQGGQQLFQKRPDI 65 (161)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcCC
Confidence 3579999999998776 678889999999999999999999999999888863
No 101
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=34.98 E-value=44 Score=28.14 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCcc
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (203)
..+||+..||..|-. -+.+|.-|...-+.+.+|-+..|.++.++-|+..|+
T Consensus 15 ~gRyls~~eL~~l~~-~~~~a~~rl~aa~~L~~na~~iV~~A~~~l~~~~P~ 65 (164)
T CHL00173 15 AGRFPSSSDLESVQG-NIQRAAARLEAAEKLASNHEAVVKEAGDACFAKYSY 65 (164)
T ss_pred ccCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 357999999999754 467899999999999999999999999999998885
No 102
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=33.88 E-value=44 Score=28.29 Aligned_cols=52 Identities=19% Similarity=0.330 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (203)
..+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|+++.++-|...|++
T Consensus 15 ~gRyls~~EL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~l 66 (172)
T CHL00171 15 RGEFLSNTQLDALSKM-VAEGNKRLDAVNKINANASTIVTNAARSLFAEQPQL 66 (172)
T ss_pred ccCCCCHHHHHHHHHH-HHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcCc
Confidence 3579999999998776 677888988888999999999999999999888853
No 103
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=33.00 E-value=65 Score=27.08 Aligned_cols=52 Identities=12% Similarity=0.206 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhhhhhCCHHHHHHHHHHHHhhCccH
Q 028836 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (203)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (203)
..+|++..||..|.. -+..|..|-..-+.+.+|...-|.++.++-|+..|+.
T Consensus 14 qgRyls~~eL~~l~~-~~~~g~~RL~aa~~Lt~na~~IV~~Aa~~lf~~~P~~ 65 (161)
T TIGR01338 14 QGRFLSNGELQSIFG-RFQRATASLEAAKSLTSNAQRLISGAAQAVYSKFPYT 65 (161)
T ss_pred ccCCCCHHHHHHHHH-HHHchHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcCc
Confidence 357999999999865 4688999999999999999999999999999988853
No 104
>PRK08609 hypothetical protein; Provisional
Probab=31.85 E-value=28 Score=34.28 Aligned_cols=32 Identities=25% Similarity=0.357 Sum_probs=24.4
Q ss_pred HhhCccHHHHHHH--hhcccCcChHHHHHHHhhh
Q 028836 98 FKSLPDLTKAVSE--LTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 98 f~~l~dv~~Al~~--Lt~LkGVGPATASaiLa~~ 129 (203)
++.+.++.+|... +..++|+|+-|+--||...
T Consensus 110 i~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i 143 (570)
T PRK08609 110 VVDKESLKEACENGKVQALAGFGKKTEEKILEAV 143 (570)
T ss_pred CCCHHHHHHHHHhCChhhccCcchhHHHHHHHHH
Confidence 3445677777763 6689999999999998764
No 105
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=31.72 E-value=22 Score=25.15 Aligned_cols=17 Identities=29% Similarity=0.342 Sum_probs=13.0
Q ss_pred cccCcChHHHHHHHhhh
Q 028836 113 VLKGVGPATASAVLAAY 129 (203)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (203)
.+=|+||||+++.-.+.
T Consensus 17 ~v~tigPA~~Al~~~~~ 33 (77)
T PF04854_consen 17 PVFTIGPATAALYYVVR 33 (77)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35689999998876663
No 106
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=29.38 E-value=50 Score=21.04 Aligned_cols=42 Identities=21% Similarity=0.390 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhh
Q 028836 87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 87 ~~~V~~~t~~Af~~l~dv~~-Al~~Lt~LkGVGPATASaiLa~ 128 (203)
+..+......+|..+.++.. +.+.|+.++|+++.+|..|...
T Consensus 3 ~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 3 EEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINR 45 (50)
T ss_pred HHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence 34455555556655544433 4788999999999999888654
No 107
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=29.33 E-value=1.4e+02 Score=21.91 Aligned_cols=32 Identities=28% Similarity=0.431 Sum_probs=23.4
Q ss_pred hhcccCcChHHHHHHHhhhCCCCCCcccHHHHHh
Q 028836 111 LTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA 144 (203)
Q Consensus 111 Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~ 144 (203)
|+.+||||.++|-.|+..-. .-||-|=+-|..
T Consensus 29 l~~Ikglg~~~a~~I~~~R~--~g~f~s~~df~~ 60 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERE--NGPFKSLEDFIQ 60 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHH--CSS-SSHHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHh--cCCCCCHHHHHH
Confidence 67899999999999999975 448877555543
No 108
>PHA00439 exonuclease
Probab=29.02 E-value=75 Score=29.09 Aligned_cols=70 Identities=16% Similarity=0.122 Sum_probs=44.6
Q ss_pred hcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhc-CC-----C---CCCCHHHHHHHHHHHHHHHHhcCccccccccce
Q 028836 112 TVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL-GH-----S---KDYSLRQYLLFADKLQAKAKVSDIFFFKCLCTF 182 (203)
Q Consensus 112 t~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~-g~-----~---ikYt~keY~~~~~~l~~~a~el~~~~~~~~~~~ 182 (203)
--++||| -||..+|.- ||+-+..=..+. |. + .|++...=..+++.|...+.+-|.+ -.
T Consensus 191 PGVpGIG-KTA~kLL~~------~~~~~~~~~~~~sg~~~~~~~~~~~k~~~~~~~~~w~~~v~~~~k~g~~------e~ 257 (286)
T PHA00439 191 SGIPGWG-DTAEAFLEN------PYIFEQVEKVLKSGKRKGQTVTKWKKRAPEPEETLWDCIVTLGAKAGMT------EE 257 (286)
T ss_pred CCCCCcC-HHHHHHHhC------ccccchhhHHhhcccccccchhhhhccCCCccccHHHHHHHHHHHcCCC------HH
Confidence 3489999 999999975 333333222222 31 1 2444443448999999999998888 34
Q ss_pred ee----ehhhhhHHHh
Q 028836 183 QF----VVCLIVLHHL 194 (203)
Q Consensus 183 ~~----~v~~v~~~~~ 194 (203)
|+ .||=|+||.+
T Consensus 258 ~~~~q~~~ari~r~~d 273 (286)
T PHA00439 258 DAIKQAQMARILRAED 273 (286)
T ss_pred HHHHHHHHHHHhhccc
Confidence 44 6777777753
No 109
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=28.79 E-value=29 Score=30.99 Aligned_cols=20 Identities=45% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHhhcccCcChHHHHHHHhh
Q 028836 109 SELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~ 128 (203)
+.|..++||||+++-.++..
T Consensus 3 ~~L~~IpGIG~krakkLl~~ 22 (232)
T PRK12766 3 EELEDISGVGPSKAEALREA 22 (232)
T ss_pred cccccCCCcCHHHHHHHHHc
Confidence 46788999999999999998
No 110
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=27.76 E-value=32 Score=28.33 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.1
Q ss_pred HHhhcccCcChHHHHHHHhh
Q 028836 109 SELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~ 128 (203)
+-|+.|.||||..++.+=..
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~ 86 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNEL 86 (133)
T ss_pred ccchhhcccCHHHHHHHHHc
Confidence 67999999999999987554
No 111
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=26.93 E-value=1.2e+02 Score=25.95 Aligned_cols=45 Identities=22% Similarity=0.151 Sum_probs=30.8
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHhcCcccc
Q 028836 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKVSDIFFF 176 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l~~~a~el~~~~~ 176 (203)
|+-+.++-||.++|.|-+|.= + +..|+|. .+++++.++|||+.+|
T Consensus 4 i~dIA~~agvS~~TVSrvLn~--~---~~vs~~t-------------------r~rV~~~a~~lgY~pn 48 (329)
T TIGR01481 4 IYDVAREAGVSMATVSRVVNG--N---PNVKPAT-------------------RKKVLEVIKRLDYRPN 48 (329)
T ss_pred HHHHHHHhCCCHHHHHHHhCC--C---CCCCHHH-------------------HHHHHHHHHHHCCCCC
Confidence 556778889999999999962 1 3455554 3456666666666653
No 112
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=26.84 E-value=1e+02 Score=26.58 Aligned_cols=38 Identities=13% Similarity=0.135 Sum_probs=28.9
Q ss_pred ccHHHHHhhcC--CCCCCCHHHHHHHHHHHHHHHHhcCcc
Q 028836 137 MSDEAMGAALG--HSKDYSLRQYLLFADKLQAKAKVSDIF 174 (203)
Q Consensus 137 fSDEa~~~~~g--~~ikYt~keY~~~~~~l~~~a~el~~~ 174 (203)
+..|.+.|+.+ .+.+||..||..+...-+++.++|..+
T Consensus 148 iG~~~ve~Le~~~~~~k~~~~el~~i~~~y~~~~k~L~k~ 187 (189)
T PF05766_consen 148 IGQERVEWLEGPHEPRKWTIEELKAIIAIYRAKLKELKKE 187 (189)
T ss_pred HhHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 34455555554 468999999999999999999888643
No 113
>PRK09672 phage exclusion protein Lit; Provisional
Probab=26.79 E-value=1.7e+02 Score=27.30 Aligned_cols=33 Identities=18% Similarity=0.115 Sum_probs=25.6
Q ss_pred ccCcChHHHHHHHhhhCCC-------CCCcccHHHHHhhc
Q 028836 114 LKGVGPATASAVLAAYAPG-------VAPFMSDEAMGAAL 146 (203)
Q Consensus 114 LkGVGPATASaiLa~~~P~-------~~pFfSDEa~~~~~ 146 (203)
=||||.|+|.++|++.-|+ ++|=+.|+....+-
T Consensus 216 Kr~vgIaia~l~l~~l~~~~~~~g~~tHP~~~~RI~a~is 255 (305)
T PRK09672 216 KRSVGIAIALLFLQELELENKSCGKGTHPDADQRIFANLS 255 (305)
T ss_pred hhhHHHHHHHHHHHHHhccccCCCCCCCCCHHHHHHHhhh
Confidence 6899999999999986553 56777777776544
No 114
>COG5578 Predicted integral membrane protein [Function unknown]
Probab=26.50 E-value=34 Score=30.05 Aligned_cols=12 Identities=42% Similarity=0.509 Sum_probs=9.8
Q ss_pred ccCcChHHHHHH
Q 028836 114 LKGVGPATASAV 125 (203)
Q Consensus 114 LkGVGPATASai 125 (203)
.=|++||||++.
T Consensus 37 VfG~~PAT~Alf 48 (208)
T COG5578 37 VFGLMPATAALF 48 (208)
T ss_pred HHccchHHHHHH
Confidence 569999999754
No 115
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=25.94 E-value=55 Score=30.89 Aligned_cols=22 Identities=23% Similarity=0.514 Sum_probs=14.7
Q ss_pred HHHHhhcccCcChHHHHHHHhh
Q 028836 107 AVSELTVLKGVGPATASAVLAA 128 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa~ 128 (203)
..+.|++.+||||+.|-.|-..
T Consensus 317 s~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 317 SIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred CHHHHhhCCCcCHHHHHHHHHH
Confidence 3567777777777777765544
No 116
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=25.83 E-value=52 Score=29.66 Aligned_cols=32 Identities=28% Similarity=0.430 Sum_probs=25.8
Q ss_pred HHHHHHHhhcccCcChHHHHHH--HhhhCCCCCC
Q 028836 104 LTKAVSELTVLKGVGPATASAV--LAAYAPGVAP 135 (203)
Q Consensus 104 v~~Al~~Lt~LkGVGPATASai--La~~~P~~~p 135 (203)
-+.=++-||..||||+-|+=.. -+++.|+..|
T Consensus 160 eEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp 193 (254)
T KOG1918|consen 160 EEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMP 193 (254)
T ss_pred HHHHHHHHHhccCccceeeeeeeeeccCCCcccC
Confidence 4556888999999999999764 4668898766
No 117
>PHA01976 helix-turn-helix protein
Probab=25.23 E-value=51 Score=22.17 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=16.6
Q ss_pred CCCCCHHHHHHHHH------HHhhCCCCCcc
Q 028836 53 NPHINTTELSKLVR------WKLTRGKWRPR 77 (203)
Q Consensus 53 ~~~ltkdEL~~Lve------WKL~rGkfRP~ 77 (203)
...||.+||-+.+. ++.-+|+..|+
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~ 43 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEADKRLPN 43 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Confidence 45788888877765 44556666664
No 118
>COG1980 Archaeal fructose 1,6-bisphosphatase [Carbohydrate transport and metabolism]
Probab=25.21 E-value=22 Score=33.08 Aligned_cols=73 Identities=26% Similarity=0.538 Sum_probs=47.9
Q ss_pred hhCCHHHHHHHHHHHHhhCccHHHHHH-----------Hhh-cccCcChHHHHHHHhhhCCC--CCCcccHHHHHhhcCC
Q 028836 83 SSLDDSSVKSASEKAFKSLPDLTKAVS-----------ELT-VLKGVGPATASAVLAAYAPG--VAPFMSDEAMGAALGH 148 (203)
Q Consensus 83 ~sN~~~~V~~~t~~Af~~l~dv~~Al~-----------~Lt-~LkGVGPATASaiLa~~~P~--~~pFfSDEa~~~~~g~ 148 (203)
+.-+.+.|++..-+||+.-..+.+-++ .++ ++||.||-.|-.=..- .|. .+.||.|.. +
T Consensus 62 ~G~d~e~vH~lAW~aF~eat~vAk~lkLYgAGQDLL~DaFSGNvrGmGPgvAEmEf~e-RpsEPiivf~~DKT------e 134 (369)
T COG1980 62 KGVDSEEVHELAWNAFKEATEVAKKLKLYGAGQDLLKDAFSGNVRGMGPGVAEMEFTE-RPSEPIIVFMADKT------E 134 (369)
T ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHhcccccchhhhhhhhccccccCCCcceeeEeec-CCCCcEEEEEecCC------C
Confidence 345677899999999975544443332 344 6999999877544333 332 446666642 5
Q ss_pred CCCCCHHHHHHHHH
Q 028836 149 SKDYSLRQYLLFAD 162 (203)
Q Consensus 149 ~ikYt~keY~~~~~ 162 (203)
|--||+.=|..|.+
T Consensus 135 PgAfNlPl~kmFAD 148 (369)
T COG1980 135 PGAFNLPLYKMFAD 148 (369)
T ss_pred CccccchHHHHhcC
Confidence 67888888888865
No 119
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.20 E-value=63 Score=31.22 Aligned_cols=26 Identities=27% Similarity=0.433 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcCcc
Q 028836 149 SKDYSLRQYLLFADKLQAKAKVSDIF 174 (203)
Q Consensus 149 ~ikYt~keY~~~~~~l~~~a~el~~~ 174 (203)
+++||..+|.++++++|+..-+..++
T Consensus 274 ~R~yt~e~~~~~i~k~R~~~Pd~~i~ 299 (437)
T COG0621 274 KRGYTVEEYLEIIEKLRAARPDIAIS 299 (437)
T ss_pred CCCcCHHHHHHHHHHHHHhCCCceEe
Confidence 57999999999999999988877776
No 120
>COG4989 Predicted oxidoreductase [General function prediction only]
Probab=25.04 E-value=43 Score=30.85 Aligned_cols=58 Identities=14% Similarity=0.200 Sum_probs=39.8
Q ss_pred CCCCCCcccHHHHHhh------------cCCCCCCC-HHHHHHHHHHHHHHHHhcC-ccccccccceeeehhhhhHHH
Q 028836 130 APGVAPFMSDEAMGAA------------LGHSKDYS-LRQYLLFADKLQAKAKVSD-IFFFKCLCTFQFVVCLIVLHH 193 (203)
Q Consensus 130 ~P~~~pFfSDEa~~~~------------~g~~ikYt-~keY~~~~~~l~~~a~el~-~~~~~~~~~~~~~v~~v~~~~ 193 (203)
.|-..|-|.|-.+..+ +|.+.-|+ -.-|..+.+.+++.|.|.| ++ -..|-+||++||-
T Consensus 183 S~~~~~~~~DGtLd~~q~~~v~pmaWSpl~gG~~F~g~~~~q~l~~~l~~ia~e~ga~s------~~~VaiAWllR~P 254 (298)
T COG4989 183 SPLHTPMLLDGTLDYCQQLRVRPMAWSPLGGGGLFLGDDKFQRLRKVLDRIAEEYGAVS------ITAVAIAWLLRHP 254 (298)
T ss_pred ccccccccccchHHHHHHcCCCcccccccCCCccccCCcchHHHHHHHHHHHHHhCccc------HHHHHHHHHHhCc
Confidence 4555566777655432 12233333 4556788999999999998 44 6778999999984
No 121
>PRK03980 flap endonuclease-1; Provisional
Probab=23.71 E-value=45 Score=30.16 Aligned_cols=17 Identities=35% Similarity=0.593 Sum_probs=14.8
Q ss_pred cccCcChHHHHHHHhhh
Q 028836 113 VLKGVGPATASAVLAAY 129 (203)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (203)
.++||||-||.-++.-+
T Consensus 193 GI~GIG~ktA~kLi~~~ 209 (292)
T PRK03980 193 GIKGIGPKTALKLIKKH 209 (292)
T ss_pred CCCCccHHHHHHHHHHC
Confidence 48999999999999764
No 122
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=22.95 E-value=61 Score=28.16 Aligned_cols=20 Identities=30% Similarity=0.551 Sum_probs=16.9
Q ss_pred HHHhhcccCcChHHHHHHHh
Q 028836 108 VSELTVLKGVGPATASAVLA 127 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa 127 (203)
++.|++++|||+=||=-|+-
T Consensus 107 ~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 107 VKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred hHhhhcCCCCCHHHHHHHHH
Confidence 45799999999999987764
No 123
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=22.81 E-value=1.3e+02 Score=25.70 Aligned_cols=30 Identities=27% Similarity=0.433 Sum_probs=20.6
Q ss_pred HHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 028836 109 SELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (203)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (203)
+-+.++=||.++|.|-+|.= + +-.|+|.-.
T Consensus 2 ~dIA~~agVS~~TVSrvLn~--~---~~vs~~tr~ 31 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINK--D---RFVSEAITA 31 (327)
T ss_pred hhHHHHhCCcHHHHHHHhCC--C---CCCCHHHHH
Confidence 34567789999999999951 1 345665443
No 124
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=22.41 E-value=52 Score=30.22 Aligned_cols=17 Identities=35% Similarity=0.581 Sum_probs=14.9
Q ss_pred cccCcChHHHHHHHhhh
Q 028836 113 VLKGVGPATASAVLAAY 129 (203)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (203)
.++||||-||--++.-+
T Consensus 240 Gv~GIG~ktA~kli~~~ 256 (338)
T TIGR03674 240 GVKGIGPKTALKLIKEH 256 (338)
T ss_pred CCCCccHHHHHHHHHHc
Confidence 59999999999999763
No 125
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.61 E-value=94 Score=31.58 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=20.1
Q ss_pred HHHHhhcccCcChHHHHHHHhhh
Q 028836 107 AVSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 107 Al~~Lt~LkGVGPATASaiLa~~ 129 (203)
+.+.|.++.||||-+|..|.+.+
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHH
Confidence 45679999999999999998875
No 126
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=21.53 E-value=57 Score=29.13 Aligned_cols=44 Identities=20% Similarity=0.350 Sum_probs=27.0
Q ss_pred cccCcChHHHHHHHhhhCCCCCCcccHHHHHhhcC----CCCCCCHHHHHHHHH
Q 028836 113 VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG----HSKDYSLRQYLLFAD 162 (203)
Q Consensus 113 ~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g----~~ikYt~keY~~~~~ 162 (203)
.++||||-||--++.-+..- +.....+.. .+..+..+++.+++.
T Consensus 227 gv~giG~k~A~~li~~~~~~------~~~~~~l~~~~~~~~~~~~~~~~~~~f~ 274 (316)
T cd00128 227 GIPGIGPVTALKLIKKYGDI------EKDIERLKKKLYRSPEDFPLKEAREFFL 274 (316)
T ss_pred CCCCccHHHHHHHHHHcCCh------HHHHHHHHHhCccCCCcCChHHHHHHHc
Confidence 49999999999999986431 223332221 123556666666554
No 127
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=21.47 E-value=93 Score=31.02 Aligned_cols=22 Identities=32% Similarity=0.613 Sum_probs=19.4
Q ss_pred HHHhhcccCcChHHHHHHHhhh
Q 028836 108 VSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~ 129 (203)
...|+.++||||.|+-.||..+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F 563 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF 563 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc
Confidence 4678899999999999999875
No 128
>PF14307 Glyco_tran_WbsX: Glycosyltransferase WbsX
Probab=20.68 E-value=33 Score=31.28 Aligned_cols=41 Identities=12% Similarity=0.155 Sum_probs=33.8
Q ss_pred CCcccHHHHHhhcCCCC-----CCCHHHHHHHHHHHHHHHHhcCcc
Q 028836 134 APFMSDEAMGAALGHSK-----DYSLRQYLLFADKLQAKAKVSDIF 174 (203)
Q Consensus 134 ~pFfSDEa~~~~~g~~i-----kYt~keY~~~~~~l~~~a~el~~~ 174 (203)
.|||+|+-|.-+.|.|+ --++.+..++++.+|+.|++.|+.
T Consensus 145 ~~~F~D~rYikVdGKPv~~Iy~p~~~pd~~~~~~~wr~~a~~~G~~ 190 (345)
T PF14307_consen 145 LPYFKDPRYIKVDGKPVFLIYRPGDIPDIKEMIERWREEAKEAGLP 190 (345)
T ss_pred HHHhCCCCceeECCEEEEEEECcccccCHHHHHHHHHHHHHHcCCC
Confidence 48999999988888663 235578889999999999999987
No 129
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=20.67 E-value=1.3e+02 Score=30.55 Aligned_cols=36 Identities=22% Similarity=0.352 Sum_probs=0.0
Q ss_pred ccHHHHHHHhhc--ccCcChHHHHHHHhhhCCCCCCcccHHHHHhh
Q 028836 102 PDLTKAVSELTV--LKGVGPATASAVLAAYAPGVAPFMSDEAMGAA 145 (203)
Q Consensus 102 ~dv~~Al~~Lt~--LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~ 145 (203)
++...-+.-|+. .+||||.||..|... |.++++..+
T Consensus 75 ~~~~~i~~yL~s~~~~GIG~~~A~~iv~~--------fg~~~~~~i 112 (720)
T TIGR01448 75 TSKEGIVAYLSSRSIKGVGKKLAQRIVKT--------FGEAAFDVL 112 (720)
T ss_pred CCHHHHHHHHhcCCCCCcCHHHHHHHHHH--------hCHhHHHHH
No 130
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=20.55 E-value=1.4e+02 Score=30.12 Aligned_cols=21 Identities=38% Similarity=0.591 Sum_probs=18.4
Q ss_pred HHhhcccCcChHHHHHHHhhh
Q 028836 109 SELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~ 129 (203)
..|..++||||.++=++|.-+
T Consensus 552 S~L~~IpGIG~kr~~~LL~~F 572 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHF 572 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHc
Confidence 567799999999999999874
No 131
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=20.14 E-value=1.2e+02 Score=30.49 Aligned_cols=22 Identities=36% Similarity=0.604 Sum_probs=19.5
Q ss_pred HHHhhcccCcChHHHHHHHhhh
Q 028836 108 VSELTVLKGVGPATASAVLAAY 129 (203)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~ 129 (203)
-..|..++||||.||-+||.-+
T Consensus 568 ~s~L~~I~GIG~k~a~~Ll~~F 589 (621)
T PRK14671 568 QTELTDIAGIGEKTAEKLLEHF 589 (621)
T ss_pred hhhhhcCCCcCHHHHHHHHHHc
Confidence 4577899999999999999986
Done!